Contacts of the helix formed by residues 89 - 108 (chain A) in PDB entry 1XTQ
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 SER 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 4.9 4.0 - - - -
86A SER* 3.0 16.6 + - - +
87A VAL 3.3 1.8 - - - -
88A THR* 1.3 83.8 - - - +
90A ILE* 1.3 61.7 + - - +
91A LYS* 3.5 10.2 + - - +
92A SER* 2.9 49.5 + - - -
93A PHE* 3.3 6.2 + - - +
128A VAL* 3.5 2.2 - - - +
129A ILE* 4.1 1.3 - - - +
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Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 1.3 72.1 - - - +
91A LYS* 1.3 64.0 + - - +
93A PHE* 3.1 4.9 + - + +
94A GLU* 2.9 34.3 + - + +
128A VAL* 3.8 25.4 - - + +
129A ILE* 3.7 24.9 - - + -
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.4 35.5 + - + +
66A GLU* 3.1 30.1 + - - +
89A SER* 3.1 8.7 - - - +
90A ILE* 1.3 79.9 - - - +
92A SER* 1.3 57.3 + - - +
94A GLU* 3.2 8.3 + - + -
95A VAL* 2.9 44.8 + - + +
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.8 21.9 - - - +
17A VAL* 3.4 29.2 - - - -
84A VAL 5.1 0.3 - - - +
85A TYR* 3.5 4.1 - - - +
86A SER 2.9 24.0 + - - -
89A SER* 2.9 30.7 + - - -
91A LYS* 1.3 77.1 - - - +
93A PHE* 1.3 56.8 + - - +
95A VAL* 3.8 1.3 - - - +
96A ILE* 3.0 28.2 + - - +
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 3.6 43.7 - + + -
89A SER 3.3 8.3 + - - +
90A ILE* 3.1 10.7 + - + +
92A SER* 1.3 79.1 + - - +
94A GLU* 1.3 70.7 + - - +
95A VAL 3.1 0.2 - - - -
96A ILE* 3.0 21.0 - - + +
97A LYS* 3.4 29.8 + - - +
129A ILE* 3.8 27.4 - - + -
133A GLU* 3.7 34.8 - - + -
134A GLY* 4.2 6.3 - - - -
137A LEU* 3.5 29.8 - - + -
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 5.9 0.9 - - - +
90A ILE* 2.9 29.8 + - + +
91A LYS* 3.8 10.3 - - + +
93A PHE* 1.3 84.2 - - + +
95A VAL* 1.3 61.9 + - + +
97A LYS* 3.0 51.0 + - - +
98A VAL* 3.5 15.8 + - - +
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.8 29.2 - - + -
64A GLN 3.8 5.8 - - - +
65A ASP* 3.9 12.1 - - - -
66A GLU* 3.5 17.0 - - - +
91A LYS* 2.9 47.4 + - + +
92A SER* 3.8 4.5 - - - +
94A GLU* 1.3 75.3 - - + +
96A ILE* 1.3 60.6 + - - +
97A LYS 3.1 1.8 - - - -
98A VAL* 3.1 8.7 + - - +
99A ILE* 2.9 44.5 + - + +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY* 4.0 4.5 - - - -
14A TYR 5.1 0.4 - - - +
83A LEU* 3.5 42.0 - - + -
84A VAL 3.7 20.0 - - - +
85A TYR* 4.3 4.9 - - + -
92A SER 3.0 14.6 + - - +
93A PHE* 3.0 27.4 - - + +
95A VAL* 1.3 77.8 - - - +
97A LYS* 1.3 58.2 + - - +
99A ILE* 3.7 20.4 - - + +
100A HIS* 3.0 27.2 + - - +
116A LEU* 4.1 15.5 - - + -
137A LEU* 4.0 21.8 - - + -
141A TRP* 3.8 1.8 - - + -
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.6 33.5 - - - +
94A GLU* 3.0 44.0 + - - +
95A VAL 3.1 0.4 - - - -
96A ILE* 1.3 78.8 - - - +
98A VAL* 1.3 63.5 + - + +
100A HIS* 3.3 4.9 + - - +
101A GLY* 3.1 18.2 + - - -
137A LEU* 4.0 29.4 - - + -
141A TRP* 4.1 9.1 - - + +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP 4.9 0.4 - - - +
66A GLU* 3.9 41.7 - - + +
94A GLU 3.6 14.1 - - - +
95A VAL* 3.1 8.2 + - - +
97A LYS* 1.3 74.3 - - + +
99A ILE* 1.3 60.8 + - + +
101A GLY* 3.1 3.0 + - - +
102A LYS* 2.9 43.8 + - + +
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.0 25.6 - - + -
13A GLY* 3.8 18.2 - - - -
64A GLN* 3.6 38.1 - - + +
65A ASP 4.9 6.1 - - - +
70A PHE* 3.5 20.6 - - + -
83A LEU* 4.4 4.3 - - + -
95A VAL* 2.9 38.5 + - + +
96A ILE* 3.7 15.5 - - + +
98A VAL* 1.3 77.4 - - - +
100A HIS* 1.3 57.8 + - - +
102A LYS* 3.3 2.4 + - - -
103A LEU* 2.9 28.2 + - - +
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Residues in contact with HIS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.8 9.2 - - + -
96A ILE 3.0 10.9 + - - +
97A LYS 3.5 2.8 + - - +
98A VAL 3.2 0.2 - - - -
99A ILE* 1.3 75.8 - - - +
101A GLY* 1.3 64.5 + - - +
103A LEU* 3.3 4.8 + - - +
104A LEU* 3.0 52.7 + - + +
114A ILE* 3.4 34.3 - - + +
141A TRP* 3.3 79.2 + + + +
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Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LYS 3.1 13.9 + - - -
98A VAL* 3.1 3.8 + - - -
100A HIS* 1.3 80.9 + - - +
102A LYS* 1.3 61.1 + - - +
104A LEU* 3.4 7.7 + - - +
105A ASP* 3.1 30.1 + - - +
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP 3.9 11.0 - - - +
66A GLU 3.3 27.4 + - - -
67A TYR 4.8 1.0 - - - -
68A SER 3.2 22.4 + - - +
70A PHE* 3.5 35.4 - - + -
98A VAL* 2.9 30.0 + - + +
99A ILE* 4.7 1.1 - - - -
101A GLY* 1.3 76.1 - - - +
103A LEU* 1.3 57.7 + - - +
105A ASP* 3.1 11.2 + - - +
106A MET* 2.9 43.2 + - + +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.2 11.2 - - + -
70A PHE* 3.4 21.3 - - + -
74A TYR* 4.7 3.6 - - + +
75A SER* 5.9 0.7 - - - -
81A TYR* 3.5 50.7 - - + +
83A LEU* 4.2 8.3 - - + -
99A ILE 2.9 17.9 + - - +
100A HIS 3.5 4.9 - - - +
101A GLY 3.2 0.2 - - - -
102A LYS* 1.3 77.6 - - - +
104A LEU* 1.3 60.9 + - - +
106A MET* 3.2 2.6 + - + -
107A VAL* 3.0 34.7 + - + +
112A ILE* 3.5 24.5 - - + -
114A ILE* 3.9 15.0 - - + -
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A HIS* 3.0 49.9 + - + +
101A GLY* 3.7 7.6 - - - +
103A LEU* 1.3 76.9 - - + +
105A ASP* 1.3 59.5 + - - +
107A VAL* 4.0 4.0 - - + -
108A GLY* 2.8 42.7 + - - +
111A GLN* 6.1 3.4 - - - +
112A ILE* 4.6 22.7 - - + +
114A ILE* 4.9 1.1 - - + -
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLY 3.1 19.6 + - - +
102A LYS* 3.1 13.3 + - - +
104A LEU* 1.3 80.5 - - - +
106A MET* 1.3 69.2 + - + +
108A GLY* 3.9 5.5 + - - -
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Residues in contact with MET 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ILE* 5.1 7.0 - - + -
70A PHE* 3.7 54.5 - - + +
75A SER* 5.0 15.9 + - - +
102A LYS* 2.9 31.8 + - + +
103A LEU* 3.2 4.9 + - + +
105A ASP* 1.3 85.5 - - + +
107A VAL* 1.3 62.7 + - + +
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER* 4.2 13.7 - - - +
81A TYR* 3.9 21.5 - - - +
103A LEU* 3.0 26.4 + - + +
104A LEU* 3.8 10.3 - - + +
106A MET* 1.3 79.7 - - + +
108A GLY* 1.3 69.3 + - - +
110A VAL* 3.2 28.1 - - + +
111A GLN 5.8 0.2 - - - +
112A ILE* 3.9 31.4 - - + +
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Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 2.8 32.5 + - - +
105A ASP 3.9 4.9 + - - -
106A MET 3.6 1.6 - - - -
107A VAL* 1.3 81.5 - - - +
109A LYS* 1.3 63.3 + - - +
110A VAL 3.4 4.4 + - - -
111A GLN 5.1 0.5 + - - -
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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
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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) + - + + + + + -
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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