Contacts of the helix formed by residues 84 - 99 (chain S) in PDB entry 6AVO
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 THR 84 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105M GLU* 4.8 10.3 + - - +
49S LYS* 4.4 7.0 - - - +
50S THR* 4.5 1.1 - - - -
82S ALA 4.6 4.7 - - - +
83S MET* 1.3 78.5 - - - +
85S THR* 1.3 61.8 + - - +
86S GLY* 3.2 12.9 + - - -
87S ALA* 3.3 14.2 + - - +
88S ILE* 3.0 24.5 + - - +
114S ASP* 5.5 0.7 - - - -
115S GLU* 2.9 47.1 - - + +
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Residues in contact with THR 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S LYS* 3.9 0.6 + - - +
50S THR* 3.2 18.8 + - - -
84S THR* 1.3 74.1 - - - +
86S GLY* 1.3 61.7 + - - +
88S ILE* 3.8 3.3 - - - +
89S ALA* 2.9 26.7 + - - +
110S ILE* 4.2 17.2 - - + +
112S GLY* 3.9 3.6 - - - +
113S LEU 3.4 34.3 + - - -
114S ASP* 4.6 6.2 - - - +
120S ALA* 4.7 12.8 - - + +
122S TYR* 3.4 28.5 - - + -
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Residues in contact with GLY 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M TYR 4.6 1.1 - - - -
104M ASN* 4.7 10.2 + - - +
84S THR* 3.2 7.2 + - - -
85S THR* 1.3 77.4 - - - +
87S ALA* 1.3 62.8 + - - +
89S ALA* 3.1 6.5 + - - +
90S ALA* 3.0 22.4 + - - +
114S ASP* 5.6 3.8 - - - +
122S TYR* 4.3 15.6 + - - -
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Residues in contact with ALA 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M TYR* 3.3 29.1 + - + +
105M GLU* 4.5 14.6 - - + +
75S TYR* 5.2 0.2 - - + -
83S MET* 3.2 35.2 - - + +
84S THR* 3.3 15.3 + - - +
86S GLY* 1.3 74.4 - - - +
88S ILE* 1.3 58.4 + - - +
90S ALA* 3.2 0.9 + - - +
91S MET* 2.8 27.7 + - - +
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Residues in contact with ILE 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S LEU* 3.9 15.9 - - + -
47S THR* 4.4 6.7 - - + -
50S THR* 3.6 31.4 - - + +
68S ILE* 4.7 10.1 - - + -
72S LEU* 3.7 21.3 - - + -
83S MET* 3.5 30.5 - - + +
84S THR 3.0 24.0 + - - +
85S THR* 3.9 4.5 - - - +
87S ALA* 1.3 76.1 - - - +
89S ALA* 1.3 62.8 + - - +
91S MET* 4.1 2.9 - - + +
92S LEU* 2.9 23.8 + - + +
110S ILE* 3.8 20.9 - - + -
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Residues in contact with ALA 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85S THR 2.9 20.5 + - - +
86S GLY 3.3 4.7 - - - +
88S ILE* 1.3 77.1 - - - +
90S ALA* 1.3 64.1 + - - +
92S LEU 3.2 1.9 + - - -
93S SER* 3.0 19.8 + - - -
110S ILE* 4.6 3.3 - - + +
122S TYR* 3.6 41.3 - - + -
124S PHE* 3.6 19.7 - - + -
130S TYR* 4.5 7.3 - - + -
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Residues in contact with ALA 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ARG* 5.3 2.9 - - - +
101M PHE 4.9 2.7 - - - +
102M THR 3.4 13.0 - - - +
103M TYR 4.0 0.4 - - - -
104M ASN* 3.4 37.9 - - + +
86S GLY 3.0 9.5 + - - +
87S ALA 3.9 2.7 - - - +
89S ALA* 1.3 76.4 - - - +
91S MET* 1.3 58.3 + - - +
93S SER* 2.8 23.9 + - - -
94S THR* 3.0 16.3 + - + +
130S TYR* 4.4 10.2 - - + +
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Residues in contact with MET 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102M THR 3.3 7.3 + - - -
103M TYR* 3.6 25.6 - - + -
68S ILE* 4.2 19.7 - - + +
71S ARG* 3.4 42.2 - - + +
72S LEU* 4.3 6.5 - - + -
83S MET* 3.4 36.8 - - + +
87S ALA 2.8 15.7 + - - +
88S ILE* 4.1 6.7 - - - +
90S ALA* 1.3 77.5 - - - +
92S LEU* 1.3 58.9 + - + +
94S THR* 3.0 8.5 + - - +
95S ILE* 2.9 37.2 + - + +
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Residues in contact with LEU 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S ILE* 3.5 4.0 - - + -
64S LEU* 4.2 11.7 - - + -
68S ILE* 3.3 40.6 - - + -
88S ILE* 2.9 20.9 + - + +
91S MET* 1.3 78.0 - - + +
93S SER* 1.3 57.8 + - - +
95S ILE* 3.9 14.4 - - + -
96S LEU* 3.0 31.0 + - + +
108S ASN* 3.3 19.7 - - - +
110S ILE* 3.3 18.2 - - + -
124S PHE* 3.2 31.2 - - + -
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Residues in contact with SER 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLN* 4.3 3.6 + - - +
54D TYR* 5.5 2.3 - - - +
89S ALA 3.0 5.7 + - - -
90S ALA* 2.8 12.6 + - - -
92S LEU* 1.3 79.9 - - - +
94S THR* 1.3 58.5 + - - +
96S LEU* 3.8 0.7 - - - -
97S TYR* 2.9 30.0 + - - +
124S PHE* 4.4 2.2 - - - -
128S GLY* 4.0 9.4 - - - -
129S SER 4.1 12.3 + - - -
130S TYR* 3.5 37.1 - - - -
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Residues in contact with THR 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D TYR* 4.5 12.0 - - + -
57D ARG* 6.6 0.2 - - - -
101M PHE* 4.2 30.5 - - + +
102M THR* 3.7 30.0 - - - +
71S ARG* 5.4 1.7 + - - -
90S ALA 3.0 10.8 + - - +
91S MET* 3.0 14.9 + - - +
93S SER* 1.3 76.7 - - - +
95S ILE* 1.3 63.2 + - - +
97S TYR* 4.3 4.3 - - - +
98S SER* 2.9 32.1 + - - -
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Residues in contact with ILE 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64S LEU* 3.5 29.4 - - + -
67S ILE* 4.0 19.5 - - + -
68S ILE* 4.4 9.2 - - + -
71S ARG* 4.0 41.1 - - + +
91S MET* 2.9 28.6 + - + +
92S LEU* 4.0 14.8 - - + +
94S THR* 1.3 77.9 + - - +
96S LEU* 1.3 62.6 + - - +
98S SER* 3.0 21.7 + - - +
99S ARG 3.9 0.7 + - - -
104S TYR* 3.8 18.0 - - + +
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Residues in contact with LEU 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64S LEU* 3.4 30.5 - - + -
92S LEU* 3.0 20.8 + - + +
95S ILE* 1.3 76.0 - - - +
97S TYR* 1.3 59.1 + - - +
99S ARG* 4.2 11.8 + - - +
104S TYR* 3.8 26.1 + - + +
106S VAL 4.8 4.0 - - - +
108S ASN* 3.2 23.8 - - - +
124S PHE* 3.4 24.5 - - + -
125S ASP 3.8 15.3 - - - +
126S PRO 3.8 9.8 - - - +
127S VAL* 3.7 15.8 - - - -
128S GLY* 3.7 17.5 - - - +
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Residues in contact with TYR 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ALA* 4.0 13.9 - - + -
51D ASP* 3.3 24.1 + - - -
54D TYR* 3.4 53.2 - + + -
55D TRP* 3.0 30.7 + + - -
95D LEU* 3.5 10.4 - - - +
93S SER* 2.9 19.8 + - - +
94S THR 4.3 1.6 - - - +
95S ILE 3.1 0.2 - - - -
96S LEU* 1.3 76.4 - - - +
98S SER* 1.3 59.5 + - - +
99S ARG 3.0 5.8 - - - -
100S ARG* 2.7 46.4 + - + +
101S PHE* 5.3 1.4 - - - -
127S VAL 3.3 21.5 - - - +
128S GLY* 4.6 1.6 - - - -
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Residues in contact with SER 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D TYR* 5.7 3.1 - - - -
94S THR 2.9 17.4 + - - -
95S ILE* 3.0 17.0 + - - +
97S TYR* 1.3 78.6 - - - +
99S ARG* 1.3 66.5 + - - +
100S ARG 3.4 1.9 + - - -
104S TYR* 5.4 0.2 - - - -
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Residues in contact with ARG 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95S ILE 3.9 1.4 + - - -
96S LEU 4.4 4.3 - - - +
97S TYR* 2.9 2.5 + - - +
98S SER* 1.3 85.1 + - - +
100S ARG* 1.3 61.8 + - - +
101S PHE 3.0 7.8 + - - -
102S PHE* 3.2 56.6 + - - +
103S PRO* 3.4 13.4 - - - +
104S TYR* 3.3 57.9 + - + +
97a TYR* 5.0 6.3 + - - -
100a ARG* 5.1 2.6 - - - +
101a SER* 4.8 19.0 + - - -
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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