Contacts of the helix formed by residues 90 - 115 (chain g) in PDB entry 6QY3
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 LYS 90 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86g GLN 3.8 5.9 + - - +
87g LEU* 3.1 18.1 + - - +
88g ASN 3.2 2.4 - - - +
89g ASP* 1.3 79.1 - - + +
91g PRO* 1.3 64.1 - - - +
92g GLU* 3.3 1.1 - - + +
93g VAL* 4.2 19.7 - - + +
94g ARG* 3.4 11.6 + - - +
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Residues in contact with PRO 91 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88g ASN 4.7 2.8 - - - +
89g ASP 4.0 2.8 - - - -
90g LYS* 1.3 71.7 - - - +
92g GLU* 1.3 59.2 + - - +
94g ARG* 3.6 5.2 + - + +
95g SER* 2.9 29.3 + - - -
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Residues in contact with GLU 92 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Z ASN* 4.6 21.5 - - + -
90g LYS* 3.3 1.9 - - + +
91g PRO* 1.3 75.3 - - - +
93g VAL* 1.3 60.8 + - - +
95g SER* 3.2 7.8 + - - -
96g GLU* 2.9 28.6 + - - +
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Residues in contact with VAL 93 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107f ILE* 6.2 4.3 - - + -
87g LEU* 5.3 4.3 - - + +
90g LYS* 3.7 20.0 + - + +
92g GLU* 1.3 78.2 - - - +
94g ARG* 1.3 58.0 + - - +
96g GLU* 3.2 7.9 + - - +
97g ILE* 2.9 28.1 + - - +
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Residues in contact with ARG 94 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87g LEU* 3.7 18.7 + - + +
88g ASN* 5.2 3.6 - - - -
90g LYS 3.4 17.3 + - - +
91g PRO* 3.9 4.9 - - + +
92g GLU 3.3 0.2 - - - -
93g VAL* 1.3 78.4 - - - +
95g SER* 1.3 56.5 + - - +
97g ILE* 3.3 8.1 + - - +
98g ASP* 2.9 27.9 + - - +
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Residues in contact with SER 95 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91g PRO 2.9 19.0 + - - -
92g GLU* 3.2 8.5 + - - -
94g ARG* 1.3 74.1 - - - +
96g GLU* 1.3 61.0 + - - +
98g ASP* 3.2 8.3 + - - +
99g SER* 2.9 27.0 + - - -
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Residues in contact with GLU 96 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92g GLU 2.9 12.7 + - - +
93g VAL* 3.2 11.0 + - - +
95g SER* 1.3 75.9 - - - +
97g ILE* 1.3 58.5 + - - +
99g SER* 3.2 8.8 + - - -
100g LEU* 2.9 29.3 + - - +
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Residues in contact with ILE 97 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104f ILE* 6.4 3.8 - - + -
107f ILE* 6.2 4.5 - - + -
93g VAL 2.9 16.3 + - - +
94g ARG* 3.6 9.4 - - - +
95g SER 3.3 0.2 - - - -
96g GLU* 1.3 76.5 - - - +
98g ASP* 1.3 56.7 + - - +
100g LEU* 3.5 6.2 + - - +
101g VAL* 2.9 31.5 + - - +
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Residues in contact with ASP 98 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94g ARG 2.9 14.2 + - - +
95g SER* 3.2 11.6 + - - +
97g ILE* 1.3 77.0 - - - +
99g SER* 1.3 56.3 + - - +
101g VAL* 3.8 5.5 - - - +
102g SER* 2.9 29.5 + - - -
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Residues in contact with SER 99 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95g SER 2.9 12.9 + - - -
96g GLU* 3.2 12.1 + - - -
98g ASP* 1.3 75.0 - - - +
100g LEU* 1.3 60.7 + - - +
102g SER* 3.1 7.4 + - - -
103g LEU* 2.9 27.7 + - - +
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Residues in contact with LEU 100 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100f LEU* 5.1 22.2 - - + +
103f LEU* 5.9 3.6 - - + -
104f ILE* 5.5 10.1 - - + +
96g GLU 2.9 15.5 + - - +
97g ILE* 4.0 7.0 - - - +
99g SER* 1.3 76.5 - - - +
101g VAL* 1.3 57.1 + - - +
103g LEU* 3.1 8.8 + - - +
104g ILE* 2.9 29.3 + - - +
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Residues in contact with VAL 101 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97g ILE 2.9 19.4 + - - +
98g ASP* 3.9 6.5 - - - +
100g LEU* 1.3 76.7 - - - +
102g SER* 1.3 57.5 + - - +
104g ILE* 4.0 5.6 - - - +
105g THR* 2.9 31.2 + - - -
124g ILE* 5.1 21.1 - - + +
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Residues in contact with SER 102 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98g ASP 2.9 19.4 + - - -
99g SER* 3.1 8.7 + - - -
101g VAL* 1.3 74.9 - - - +
103g LEU* 1.3 59.8 + - - +
105g THR* 3.5 6.6 + - - -
106g ASP* 2.9 28.4 + - - +
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Residues in contact with LEU 103 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100f LEU* 5.9 4.9 - - + -
99g SER 2.9 12.5 + - - +
100g LEU* 3.1 11.0 + - - +
102g SER* 1.3 74.1 - - - +
104g ILE* 1.3 60.2 + - - +
106g ASP* 3.1 7.8 + - - +
107g ILE* 2.9 28.6 + - - +
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Residues in contact with ILE 104 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97f ILE* 6.4 2.7 - - + -
100f LEU* 5.4 9.9 - - + -
100g LEU 2.9 14.5 + - - +
101g VAL* 4.0 6.5 - - - +
103g LEU* 1.3 76.5 - - - +
105g THR* 1.3 58.1 + - - +
107g ILE* 3.2 6.3 + - - +
108g ILE* 2.9 31.5 + - - +
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Residues in contact with THR 105 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101g VAL 2.9 20.3 + - - -
102g SER* 3.8 6.5 - - - -
104g ILE* 1.3 77.1 - - - +
106g ASP* 1.3 55.9 + - - +
108g ILE* 4.4 4.2 - - - +
109g MET* 2.9 31.7 + - - +
123g GLU* 6.5 1.1 - - - -
124g ILE* 6.0 6.5 - - - -
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Residues in contact with ASP 106 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102g SER 2.9 18.1 + - - +
103g LEU* 3.1 8.5 + - - +
105g THR* 1.3 75.1 - - - +
107g ILE* 1.3 59.5 + - - +
109g MET* 3.4 5.6 + - - +
110g ALA* 2.9 29.5 + - - +
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Residues in contact with ILE 107 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93f VAL* 6.3 2.7 - - + -
97f ILE* 6.1 5.4 - - + -
103g LEU 2.9 14.3 + - - +
104g ILE* 3.2 8.0 + - - +
106g ASP* 1.3 77.0 - - - +
108g ILE* 1.3 57.7 + - - +
110g ALA* 3.1 7.1 + - - +
111g GLU* 2.9 28.3 + - - +
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Residues in contact with ILE 108 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130f ILE* 6.5 1.3 - - + -
133f LEU* 6.0 5.8 - - + -
104g ILE 2.9 16.8 + - - +
105g THR* 4.4 4.5 - - - +
107g ILE* 1.3 76.2 - - - +
109g MET* 1.3 57.1 + - - +
111g GLU* 3.4 8.0 + - - +
112g CYS* 2.9 28.1 + - - +
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Residues in contact with MET 109 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105g THR 2.9 22.6 + - - +
106g ASP* 3.7 6.5 - - - +
107g ILE 3.2 0.2 - - - -
108g ILE* 1.3 75.6 - - - +
110g ALA* 1.3 59.3 + - - +
112g CYS* 3.2 7.3 + - - +
113g ILE* 2.9 28.2 + - - +
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Residues in contact with ALA 110 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106g ASP 2.9 18.2 + - - +
107g ILE* 3.1 6.7 + - - +
109g MET* 1.3 77.1 - - - +
111g GLU* 1.3 57.9 + - - +
113g ILE* 3.2 8.0 + - - +
114g GLU* 2.9 27.9 + - - +
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Residues in contact with GLU 111 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83f ILE* 5.7 5.8 - - + +
86f GLN* 5.7 11.3 - - + +
87f LEU* 5.7 9.9 - - + +
107g ILE 2.9 15.4 + - - +
108g ILE* 3.8 8.3 - - - +
110g ALA* 1.3 76.3 - - - +
112g CYS* 1.3 60.9 + - - +
114g GLU* 3.3 15.8 + - - +
115g ASN* 3.4 12.1 + - - +
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Residues in contact with CYS 112 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108g ILE 2.9 18.3 + - - +
109g MET* 3.5 9.0 - - - +
110g ALA 3.2 0.2 - - - -
111g GLU* 1.3 75.4 - - - +
113g ILE* 1.3 63.1 + - - +
115g ASN* 3.3 23.0 + - - +
117g LEU 4.2 6.9 - - - +
119g ILE* 4.1 25.2 + - + +
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Residues in contact with ILE 113 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109g MET 2.9 16.1 + - - +
110g ALA* 3.2 8.3 + - - +
112g CYS* 1.3 75.9 - - - +
114g GLU* 1.3 62.6 + - - +
115g ASN 3.4 6.8 + - - +
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Residues in contact with GLU 114 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110g ALA 2.9 12.9 + - - +
111g GLU* 3.6 13.7 - - - +
112g CYS 3.2 0.2 - - - -
113g ILE* 1.3 78.3 - - - +
115g ASN* 1.3 60.8 + - - +
116g GLU* 3.8 0.3 + - - -
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Residues in contact with ASN 115 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111g GLU 3.4 8.9 + - - +
112g CYS* 3.3 17.2 + - - +
113g ILE 3.2 10.0 - - - +
114g GLU* 1.3 82.0 - - - +
116g GLU* 1.3 63.8 + - - +
117g LEU* 3.3 14.4 + - + +
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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