Contacts of the helix formed by residues 85 - 110 (chain m) in PDB entry 5XTD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 85 (chain m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23k ARG* 4.2 15.0 - - - -
80m GLU* 5.4 3.3 - - - +
81m ALA 4.3 1.6 + - - -
83m GLY 3.1 14.2 - - - +
84m SER* 1.3 84.7 + - - +
86m VAL* 1.3 63.9 + - - -
87m GLU 3.6 0.7 - - - -
88m VAL* 3.9 19.1 - - - +
89m LEU* 3.7 14.4 + - - +
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Residues in contact with VAL 86 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23k ARG* 4.6 2.0 - - - +
84m SER 4.9 3.6 - - - +
85m GLY* 1.3 72.5 - - - -
87m GLU* 1.3 64.0 + - + +
88m VAL 3.1 1.9 + - - -
89m LEU* 3.2 8.6 + - - +
90m VAL* 2.9 40.4 + - + +
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Residues in contact with GLU 87 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21k VAL* 5.2 7.5 - - - +
23k ARG* 3.7 37.5 - - - +
86m VAL* 1.3 79.4 - - + +
88m VAL* 1.3 57.2 + - - +
90m VAL* 3.4 12.4 - - + +
91m SER* 2.9 30.0 + - - -
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Residues in contact with VAL 88 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23k ARG* 4.0 18.6 - - - +
21m SER* 3.8 34.1 - - - +
22m LYS 4.7 1.1 - - - +
23m PRO* 5.1 7.6 - - + -
80m GLU* 4.2 14.8 - - - +
81m ALA 4.8 5.2 - - - +
82m TRP* 3.5 28.3 - - + +
85m GLY* 3.9 19.7 - - - +
86m VAL 3.1 0.2 - - - -
87m GLU* 1.3 76.8 - - - +
89m LEU* 1.3 61.7 + - - +
91m SER* 2.6 22.9 + - - -
92m VAL* 2.9 16.6 + - + +
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Residues in contact with LEU 89 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82m TRP 3.3 23.6 - - - +
83m GLY* 3.3 28.9 - - - +
85m GLY 3.7 10.3 - - - +
86m VAL* 3.2 9.0 + - - +
88m VAL* 1.3 75.3 - - + +
90m VAL* 1.3 63.1 + - + +
92m VAL* 3.3 11.3 + - + +
93m LEU* 3.0 36.9 + - + +
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Residues in contact with VAL 90 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86m VAL* 2.9 32.7 + - + +
87m GLU* 3.4 14.6 - - + +
89m LEU* 1.3 76.6 - - - +
91m SER* 1.3 59.1 + - - +
93m LEU* 3.1 11.1 + - + +
94m VAL* 2.9 41.9 + - + +
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Residues in contact with SER 91 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17m VAL* 4.3 3.5 - - - +
20m SER 5.2 2.0 - - - -
21m SER* 3.1 27.9 + - - -
87m GLU 2.9 13.7 + - - -
88m VAL* 2.6 19.8 + - - -
90m VAL* 1.3 77.5 - - - +
92m VAL* 1.3 56.8 + - - +
94m VAL* 3.2 10.5 + - - +
95m GLY* 2.9 24.6 + - - -
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Residues in contact with VAL 92 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17m VAL* 3.8 18.6 - - + +
18m GLY* 5.1 3.1 - - - +
21m SER* 3.9 19.3 - - - +
82m TRP* 5.6 5.2 - - + +
88m VAL* 2.9 26.8 + - + +
89m LEU* 3.7 15.5 - - + +
91m SER* 1.3 76.9 + - - +
93m LEU* 1.3 65.9 + - + +
95m GLY* 3.0 2.8 + - - -
96m LEU* 3.0 38.3 + - + +
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Residues in contact with LEU 93 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89m LEU* 3.0 28.2 + - + +
90m VAL* 3.6 7.2 - - - +
92m VAL* 1.3 79.3 - - + +
94m VAL* 1.3 57.8 + - + +
96m LEU* 3.4 17.7 + - + +
97m ALA* 2.9 28.8 + - - +
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Residues in contact with VAL 94 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17k LEU* 6.0 7.2 - - + -
90m VAL* 2.9 31.5 + - + +
91m SER* 3.5 10.1 - - - +
92m VAL 3.2 0.2 - - - -
93m LEU* 1.3 77.3 - - + +
95m GLY* 1.3 57.9 + - - +
97m ALA* 3.2 9.1 + - + +
98m MET* 2.9 37.6 + - + +
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Residues in contact with GLY 95 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14k ILE* 5.1 4.5 - - - -
17m VAL* 3.6 27.2 - - - +
91m SER 2.9 11.6 + - - -
92m VAL 3.0 4.4 + - - -
94m VAL* 1.3 75.8 - - - +
96m LEU* 1.3 64.2 + - - +
98m MET* 3.0 10.0 + - - +
99m GLU* 2.9 28.5 + - - +
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Residues in contact with LEU 96 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14m MET* 4.0 18.6 - - + -
17m VAL* 5.1 5.2 - - + -
92m VAL* 3.0 27.5 + - + +
93m LEU* 3.9 17.9 - - + +
95m GLY* 1.3 75.1 - - - +
97m ALA* 1.3 56.9 + - - +
99m GLU* 3.2 29.2 - - - +
100m VAL* 3.0 39.1 + - + +
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Residues in contact with ALA 97 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93m LEU 2.9 18.6 + - - +
94m VAL* 3.3 12.1 - - + +
95m GLY 3.1 0.2 - - - -
96m LEU* 1.3 77.8 - - - +
98m MET* 1.3 58.9 + - + +
100m VAL* 5.3 0.9 - - - -
101m GLY* 2.9 26.0 + - - +
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Residues in contact with MET 98 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10k LEU* 4.1 37.3 - - + +
13k THR* 5.8 2.2 - - - +
14k ILE* 5.0 7.4 - - + -
17k LEU* 6.2 5.2 - - + -
94m VAL* 2.9 27.8 + - + +
95m GLY* 3.0 9.4 + - - +
97m ALA* 1.3 77.5 - - - +
99m GLU* 1.3 69.5 + - - +
101m GLY* 4.6 0.4 - - - -
102m LEU* 2.9 37.3 + - + +
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Residues in contact with GLU 99 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10k LEU* 5.2 5.2 - - + -
10m VAL* 5.1 9.4 - - + +
13m VAL* 3.4 34.1 - - + +
14m MET* 3.1 31.4 - - - +
17m VAL* 3.6 11.8 - - - +
95m GLY 2.9 15.0 + - - +
96m LEU* 3.2 30.2 + - - +
98m MET* 1.3 82.0 - - + +
100m VAL* 1.3 69.6 + - + +
102m LEU* 4.5 0.5 - - - +
103m VAL* 3.0 30.0 + - + +
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Residues in contact with VAL 100 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96m LEU* 3.0 18.4 + - + +
97m ALA* 4.9 1.1 - - - +
99m GLU* 1.3 86.9 - - + +
101m GLY* 1.3 67.1 + - - +
103m VAL* 4.0 6.0 - - + +
104m LEU* 2.9 51.3 + - + +
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Residues in contact with GLY 101 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97m ALA 2.9 24.3 + - - -
98m MET* 3.5 0.9 - - - -
99m GLU 3.0 1.0 - - - -
100m VAL* 1.3 82.5 - - - +
102m LEU* 1.3 59.7 + - - -
104m LEU* 3.5 6.7 - - - +
105m TRP* 2.9 22.8 + - - +
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Residues in contact with LEU 102 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6k MET* 4.5 20.8 - - + +
10k LEU* 3.5 28.0 - - + -
98m MET* 2.9 29.8 + - + +
99m GLU 4.5 0.2 - - - +
101m GLY* 1.3 71.0 - - - -
103m VAL* 1.3 65.5 + - + +
105m TRP* 3.3 30.9 - - + +
106m VAL* 3.0 27.9 + - - +
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Residues in contact with VAL 103 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3k LEU* 5.7 4.7 - - + -
6k MET* 6.0 1.6 - - + -
6m PHE* 3.9 37.0 - - + -
10m VAL* 5.2 7.4 - - + -
99m GLU* 3.0 23.3 + - + +
100m VAL* 4.0 6.3 - - - +
102m LEU* 1.3 78.1 - - + +
104m LEU* 1.3 61.8 + - + +
106m VAL* 3.5 3.6 + - - +
107m LYS* 3.0 27.1 + - + +
119m ASN* 4.7 11.6 + - - +
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Residues in contact with LEU 104 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100m VAL* 2.9 46.1 + - + +
101m GLY* 3.5 5.4 - - - +
103m VAL* 1.3 80.7 - - + +
105m TRP* 1.3 57.6 + - - +
107m LYS* 3.2 13.9 + - + +
108m GLU* 2.9 41.9 + - + +
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Residues in contact with TRP 105 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6k MET* 5.2 6.5 - - + -
101m GLY 2.9 13.5 + - - +
102m LEU* 3.1 32.3 + - + +
104m LEU* 1.3 76.2 - - - +
106m VAL* 1.3 91.4 + - + +
108m GLU* 3.0 10.4 + - - +
109m TYR* 2.9 68.5 + + + +
113m VAL* 4.0 26.7 - - + -
114m VAL* 5.0 9.4 - - + -
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Residues in contact with VAL 106 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3k LEU* 3.7 11.7 - - + -
6k MET* 3.8 26.7 - - + -
102m LEU 3.0 16.5 + - - +
103m VAL* 4.1 3.1 - - - +
105m TRP* 1.3 97.9 - - + +
107m LYS* 1.3 66.4 + - - +
110m ASP* 2.9 36.3 + - - +
114m VAL* 4.7 7.0 - - + -
117m ASN* 3.2 33.4 - - + +
118m PHE 5.5 0.2 - - - +
119m ASN* 5.7 4.9 - - + +
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Residues in contact with LYS 107 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3m TYR* 5.4 3.2 + - - -
103m VAL* 3.0 20.6 + - + +
104m LEU* 3.3 15.7 - - + +
105m TRP 3.2 0.4 - - - -
106m VAL* 1.3 77.7 - - - +
108m GLU* 1.3 63.7 + - + +
110m ASP* 4.4 5.6 - - - +
119m ASN* 4.2 34.7 - - + +
120m SER* 3.8 20.8 + - - +
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Residues in contact with GLU 108 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104m LEU* 2.9 24.5 + - + +
105m TRP* 3.0 12.1 + - - +
107m LYS* 1.3 81.8 - - + +
109m TYR* 1.3 84.9 + - + +
110m ASP* 3.2 5.0 + - - +
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Residues in contact with TYR 109 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105m TRP* 2.9 62.2 + + + +
108m GLU* 1.3 93.4 + - + +
110m ASP* 1.3 53.8 + - - +
111m GLY 2.6 19.9 + - - -
112m VAL* 2.9 44.9 + - + +
113m VAL* 5.5 1.3 - - + -
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Residues in contact with ASP 110 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81h LYS* 4.2 19.1 + - - -
106m VAL* 2.9 29.2 + - - +
107m LYS* 4.4 5.0 - - - +
108m GLU 3.7 7.6 - - - +
109m TYR* 1.3 75.2 - - - +
111m GLY* 1.3 67.3 + - - +
112m VAL 3.2 4.2 + - - -
113m VAL* 4.1 0.5 + - - +
114m VAL* 3.1 30.4 + - - +
116m VAL* 2.8 24.6 - - - +
117m ASN* 4.9 0.2 - - - +
118m PHE* 3.0 26.0 + - - +
119m ASN 4.1 2.9 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il