Contacts of the helix formed by residues 87 - 101 (chain B) in PDB entry 2AVD
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 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLU* 5.4 7.4 - - - +
73B ARG* 5.8 0.9 - - - +
85B MET* 4.6 8.1 - - + +
86B MET* 1.3 76.0 - - - +
88B CYS* 1.3 65.6 + - - +
89B GLU* 2.7 32.0 + - - +
90B GLN* 3.0 24.8 + - - +
91B ALA* 3.0 21.1 + - - +
115B TYR* 4.2 0.2 - - - -
253B GLY* 4.2 15.3 - - - -
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Residues in contact with CYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 4.1 18.4 - - - -
63B MET* 3.6 31.8 - - + +
65B GLU* 3.8 2.0 - - - +
73B ARG* 3.8 29.6 - - - +
86B MET 3.9 0.6 + - - -
87B THR* 1.3 74.9 - - - +
89B GLU* 1.3 67.8 + - - +
91B ALA* 3.4 2.1 + - - +
92B GLN* 3.0 28.6 + - - +
115B TYR* 3.3 25.9 + - - +
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A SER* 5.0 1.0 + - - -
249A LEU 5.4 3.1 - - - +
250A LEU* 5.8 2.0 - - + +
55B TRP* 3.7 30.3 + - + -
58B LEU* 4.8 7.6 - - + -
59B LEU* 3.9 21.6 - - + +
62B SER* 5.4 2.2 - - - +
63B MET* 3.8 11.0 - - - -
87B THR* 2.7 34.6 + - - +
88B CYS* 1.3 76.0 + - - +
90B GLN* 1.3 62.5 + - - +
92B GLN* 3.9 2.8 - - - +
93B LEU* 3.0 28.4 + - - +
252B LEU* 3.7 31.9 - - + +
253B GLY 4.1 6.6 + - - -
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Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B MET* 3.8 10.7 - - + -
87B THR* 3.0 35.7 + - - +
89B GLU* 1.3 77.1 - - - +
91B ALA* 1.3 66.2 + - - +
93B LEU* 3.1 4.5 + - - +
94B LEU* 3.0 28.3 + - + +
211B LEU* 3.3 29.3 - - + +
212B ARG 5.3 0.4 - - - +
252B LEU* 3.6 39.8 + - + -
253B GLY* 3.6 18.5 - - - -
254B ASP 4.8 1.3 + - - +
255B GLY 4.4 3.4 + - - -
256B LEU* 3.7 24.4 - - + +
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 5.5 1.6 - - + -
86B MET* 3.5 21.0 - - - -
87B THR 3.0 7.9 + - - +
88B CYS 3.8 3.4 - - - +
90B GLN* 1.3 76.2 - - - +
92B GLN* 1.3 57.8 + - - +
94B LEU* 3.4 3.6 + - - +
95B ALA* 2.9 30.3 + - - +
115B TYR* 3.5 33.9 - - + +
119B ALA* 3.7 23.0 - - + +
120B LEU* 5.9 0.2 - - - +
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Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ILE* 2.9 19.1 + - - +
248A SER* 4.5 2.8 + - - +
62B SER* 2.9 31.3 + - - -
63B MET* 3.4 17.9 - - + +
64B ARG* 2.9 35.5 + - - +
65B GLU* 4.6 0.7 - - - -
88B CYS 3.0 17.2 + - - +
89B GLU* 3.9 5.8 - - - +
91B ALA* 1.3 73.6 - - - +
93B LEU* 1.3 62.5 + - - +
95B ALA* 3.8 5.3 - - + +
96B ASN* 2.8 49.1 + - - +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A SER* 3.5 29.3 + - - +
250A LEU* 4.3 10.3 - - + -
258A LEU* 4.7 13.2 - - + -
260A PHE* 4.9 3.8 - - + -
89B GLU 3.0 18.8 + - - +
90B GLN* 3.1 5.4 + - - +
92B GLN* 1.3 77.2 - - - +
94B LEU* 1.3 58.5 + - + +
96B ASN* 3.3 3.6 + - - +
97B LEU* 2.8 54.7 + - + +
250B LEU* 3.7 29.8 - - + -
252B LEU* 4.1 10.5 - - + -
256B LEU* 4.0 16.6 - - + -
258B LEU* 4.4 7.9 - - + -
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B MET* 3.6 32.5 - - + -
90B GLN* 3.0 21.0 + - + +
91B ALA* 3.8 3.6 - - - +
93B LEU* 1.3 76.1 - - + +
95B ALA* 1.3 58.8 + - - +
97B LEU* 3.2 10.7 + - + +
98B ALA* 2.9 28.1 + - - +
120B LEU* 4.5 14.9 - - + +
181B VAL* 5.4 6.4 - - + +
183B VAL* 4.2 15.5 - - + -
207B ILE* 5.2 4.7 - - + -
209B ALA* 3.8 16.2 - - + -
211B LEU* 4.3 5.6 - - + -
256B LEU* 4.7 11.0 - - + -
258B LEU* 3.7 30.3 - - + -
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ALA 2.9 18.0 + - - +
92B GLN* 3.8 7.4 - - + +
94B LEU* 1.3 71.6 - - - +
96B ASN* 1.3 62.4 + - - +
98B ALA* 3.2 1.9 + - - -
99B ARG* 2.8 27.9 + - - +
119B ALA* 3.6 26.7 - - + +
120B LEU* 4.7 4.8 - - - +
123B ALA* 3.3 20.9 - - + +
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TYR* 3.3 37.6 - - + +
247A ILE* 2.8 34.9 + - - +
248A SER* 2.9 16.8 + - - -
260A PHE* 3.7 18.4 - - + -
92B GLN* 2.8 28.9 + - - +
93B LEU* 3.4 5.6 - - - +
95B ALA* 1.3 77.9 - - - +
97B LEU* 1.3 56.7 + - - +
99B ARG* 3.3 1.0 + - - -
100B LEU* 2.8 27.3 + - - +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.8 25.8 - - + -
100A LEU* 4.9 2.7 - - + -
260A PHE* 4.1 17.3 - - + -
93B LEU* 2.8 38.4 + - + +
94B LEU* 3.2 9.4 + - + +
96B ASN* 1.3 69.2 - - - +
98B ALA* 1.3 64.8 + - - +
100B LEU* 3.2 19.7 + - + +
101B ILE* 3.1 28.4 + - - +
207B ILE* 3.7 22.2 - - + -
258B LEU* 3.8 36.1 - - + -
260B PHE* 4.9 4.9 - - + -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU 2.9 13.7 + - - +
95B ALA* 3.5 9.6 - - - +
97B LEU* 1.3 74.8 - - - +
99B ARG* 1.3 62.0 + - - +
101B ILE* 3.3 2.8 + - - +
102B GLN 3.2 3.5 + - - -
103B ALA* 2.9 45.4 + - + +
120B LEU* 4.5 9.9 - - + -
123B ALA* 4.0 13.9 - - + -
124B LEU* 4.6 5.2 - - + -
181B VAL* 4.0 17.0 - - + +
207B ILE* 4.7 0.4 - - - +
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Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A TYR* 3.6 49.7 + - + +
262A ILE* 3.6 35.2 - - - +
95B ALA 2.8 16.7 + - - +
96B ASN* 3.6 5.2 - - - +
98B ALA* 1.3 74.5 - - - +
100B LEU* 1.3 65.3 + - - +
102B GLN* 3.1 17.8 + - - +
123B ALA* 4.1 23.2 - - + +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 5.0 0.9 - - + -
100A LEU* 4.5 10.3 - - + -
101A ILE* 3.8 28.6 - - + +
205A GLY* 3.1 36.4 - - - +
207A ILE* 4.0 9.2 - - + -
246A TYR* 3.3 13.2 + - - +
260A PHE* 3.9 37.0 - - + -
96B ASN 2.8 18.5 + - - +
97B LEU* 3.3 23.1 - - + +
99B ARG* 1.3 74.9 - - - +
101B ILE* 1.3 58.8 + - + +
102B GLN* 3.5 8.0 + - - +
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Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 4.0 37.5 - - + +
101A ILE* 5.0 4.0 - - + -
97B LEU 3.1 16.7 + - - +
98B ALA* 3.5 9.2 - - - +
100B LEU* 1.3 82.0 - - + +
102B GLN* 1.3 72.9 + - - +
103B ALA* 3.3 3.2 + - + +
180B ASP* 3.5 29.2 - - + +
181B VAL* 4.1 5.2 - - + -
203B ARG* 3.6 33.3 + - - +
205B GLY 4.1 7.6 - - - +
207B ILE* 3.8 14.8 - - + -
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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
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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