Contacts of the helix formed by residues 87 - 101 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLU* 3.9 27.6 - - + +
55A TRP* 6.4 0.4 - - + -
85A MET* 3.5 3.7 + - - +
86A MET* 1.3 79.4 - - - +
88A CYS* 1.3 65.9 + - - +
89A GLU* 2.7 32.7 + - - +
90A GLN* 2.8 27.2 + - - +
91A ALA* 3.1 17.5 + - - +
253A GLY* 4.6 10.5 - - - -
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Residues in contact with CYS 88 (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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59A LEU* 4.0 22.9 - - - -
63A MET* 3.6 29.9 - - + +
65A GLU* 3.9 7.2 - - - +
73A ARG* 4.0 22.0 - - - +
86A MET 3.6 0.8 + - - -
87A THR* 1.3 72.7 - - - +
89A GLU* 1.3 61.0 + - - +
91A ALA* 3.4 2.9 + - - +
92A GLN* 2.9 28.8 + - - +
115A TYR* 3.3 27.0 + - - +
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Residues in contact with GLU 89 (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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55A TRP* 3.6 26.6 + - + -
58A LEU* 4.8 7.6 - - + -
59A LEU* 3.7 26.5 - - + +
62A SER* 5.2 3.1 - - - +
63A MET* 3.7 12.8 - - - -
87A THR* 2.7 33.3 + - - +
88A CYS* 1.3 74.8 + - - +
90A GLN* 1.3 70.0 + - - +
92A GLN* 3.9 2.5 - - - +
93A LEU* 2.9 29.5 + - - +
252A LEU* 3.8 27.2 - - + +
253A GLY 4.3 3.6 + - - -
248B SER* 4.9 1.7 + - - -
249B LEU 5.3 4.5 - - - +
250B LEU* 5.8 2.0 - - + +
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Residues in contact with GLN 90 (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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86A MET* 2.8 23.3 - - + +
87A THR* 2.8 35.2 + - - +
89A GLU* 1.3 78.2 - - - +
91A ALA* 1.3 64.0 + - - +
93A LEU* 3.2 4.4 + - - +
94A LEU* 3.0 26.7 + - - +
211A LEU* 3.2 26.1 - - - +
212A ARG* 5.3 1.1 + - - +
252A LEU* 3.6 40.1 + - + -
253A GLY* 3.6 18.5 - - - -
254A ASP 4.9 1.4 + - - +
255A GLY 4.6 2.8 + - - -
256A LEU* 3.8 18.8 - - + +
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Residues in contact with ALA 91 (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 LEU* 5.7 0.9 - - + -
86A MET* 3.4 20.2 - - - +
87A THR 3.1 4.9 + - - +
88A CYS 3.7 3.8 - - - +
90A GLN* 1.3 77.4 - - - +
92A GLN* 1.3 57.4 + - - +
94A LEU* 3.4 5.4 + - - +
95A ALA* 2.9 29.3 + - - +
115A TYR* 3.3 35.2 - - + +
116A SER* 4.9 1.6 - - - -
119A ALA* 3.8 22.4 - - + +
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Residues in contact with GLN 92 (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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62A SER* 2.8 31.3 + - - -
63A MET* 3.2 19.7 - - + +
64A ARG* 2.8 33.6 + - - +
65A GLU* 4.8 0.5 - - - -
69A LEU* 6.5 0.7 - - - -
88A CYS 2.9 18.7 + - - +
89A GLU* 3.9 4.9 - - - +
91A ALA* 1.3 74.9 - - - +
93A LEU* 1.3 59.7 + - - +
95A ALA* 3.7 6.1 - - + +
96A ASN* 2.8 49.8 + - - +
119A ALA* 5.8 0.4 - - - -
247B ILE* 2.8 20.0 + - - +
248B SER* 4.5 3.2 + - - +
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Residues in contact with LEU 93 (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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89A GLU 2.9 19.4 + - - +
90A GLN* 3.2 4.9 + - - +
92A GLN* 1.3 76.3 - - - +
94A LEU* 1.3 58.5 + - + +
96A ASN* 3.2 2.6 + - - +
97A LEU* 2.9 56.0 + - + +
250A LEU* 3.8 28.9 - - + -
252A LEU* 4.0 10.1 - - + -
256A LEU* 4.0 18.8 - - + -
258A LEU* 4.3 7.9 - - + -
248B SER* 3.5 29.1 + - - +
250B LEU* 4.3 10.8 - - + -
258B LEU* 4.7 12.1 - - + -
260B PHE* 5.0 3.8 - - + -
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Residues in contact with LEU 94 (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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86A MET* 3.6 33.2 - - + -
90A GLN 3.0 11.8 + - - +
91A ALA* 3.7 4.9 - - - +
93A LEU* 1.3 76.1 - - + +
95A ALA* 1.3 56.7 + - - +
97A LEU* 3.3 9.6 + - + +
98A ALA* 2.9 28.6 + - - +
116A SER* 6.0 0.7 - - - -
120A LEU* 4.4 15.5 - - + +
181A VAL* 5.1 6.3 - - + +
183A VAL* 4.0 26.7 - - + -
207A ILE* 5.4 4.0 - - + -
209A ALA* 3.7 26.9 - - + -
211A LEU* 4.3 2.5 - - + -
256A LEU* 4.5 9.4 - - + -
258A LEU* 3.7 19.7 - - + -
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Residues in contact with ALA 95 (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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91A ALA 2.9 17.6 + - - +
92A GLN* 3.7 7.9 - - + +
94A LEU* 1.3 74.4 - - - +
96A ASN* 1.3 60.3 + - - +
98A ALA* 3.3 3.5 + - - -
99A ARG* 2.9 25.9 + - - +
119A ALA* 3.4 29.2 - - + +
120A LEU* 4.6 5.7 - - - +
123A ALA* 3.1 20.6 - - + +
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Residues in contact with ASN 96 (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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92A GLN* 2.8 30.7 + - - +
93A LEU* 3.4 4.5 - - - +
95A ALA* 1.3 80.5 - - - +
97A LEU* 1.3 58.9 - - - +
99A ARG* 3.3 1.5 + - - -
100A LEU* 2.8 25.7 + - - +
246B TYR* 3.3 38.6 - - + +
247B ILE* 2.9 35.4 + - - +
248B SER* 3.0 15.9 + - - +
260B PHE* 3.8 18.0 - - + -
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Residues in contact with LEU 97 (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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93A LEU* 2.9 34.7 + - + +
94A LEU* 3.3 7.8 + - + +
96A ASN* 1.3 72.3 - - - +
98A ALA* 1.3 66.1 + - - +
100A LEU* 3.2 19.6 + - + +
101A ILE* 3.1 27.9 + - - +
207A ILE* 3.6 26.0 - - + -
258A LEU* 3.9 35.0 - - + -
260A PHE* 4.9 4.5 - - + -
97B LEU* 3.8 27.6 - - + -
100B LEU* 5.0 0.2 - - + -
260B PHE* 4.0 16.4 - - + -
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Residues in contact with ALA 98 (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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94A LEU 2.9 14.2 + - - +
95A ALA* 3.3 10.5 + - - +
97A LEU* 1.3 76.2 - - - +
99A ARG* 1.3 60.2 + - - +
101A ILE* 3.3 1.4 + - - +
102A GLN 3.2 3.3 + - - -
103A ALA* 2.9 46.8 + - + +
106A ALA* 6.2 0.2 - - + -
120A LEU* 4.5 10.1 - - + -
123A ALA* 4.1 12.1 - - + -
124A LEU* 4.5 5.4 - - + -
181A VAL* 3.9 18.2 - - + +
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Residues in contact with ARG 99 (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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95A ALA 2.9 13.3 + - - +
96A ASN* 3.6 7.2 - - - +
98A ALA* 1.3 72.5 - - - +
100A LEU* 1.3 68.3 + - - +
102A GLN* 3.0 19.6 + - - +
123A ALA* 3.9 25.5 - - + +
246B TYR* 3.5 50.2 + - + +
262B ILE* 3.8 32.1 - - - +
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Residues in contact with LEU 100 (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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96A ASN 2.8 18.7 + - - +
97A LEU* 3.3 23.3 - - + +
99A ARG* 1.3 74.7 - - - +
101A ILE* 1.3 59.1 + - + +
102A GLN* 3.4 9.2 + - - +
97B LEU* 4.9 1.3 - - + -
100B LEU* 4.5 11.0 - - + -
101B ILE* 4.0 27.0 - - + +
205B GLY* 3.3 35.3 - - - +
207B ILE* 4.0 11.2 - - + -
246B TYR* 3.2 13.9 + - - +
260B PHE* 3.8 39.0 - - + -
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Residues in contact with ILE 101 (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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97A LEU 3.1 18.8 + - - +
98A ALA* 3.5 9.6 - - - +
100A LEU* 1.3 80.0 - - + +
102A GLN* 1.3 73.6 + - - +
103A ALA 3.3 3.9 + - - +
180A ASP* 3.4 28.9 - - + +
181A VAL* 3.9 12.6 - - + -
203A ARG* 3.4 33.2 + - - +
205A GLY 4.1 4.9 - - - +
207A ILE* 4.0 12.1 - - + -
100B LEU* 3.8 37.2 - - + +
101B ILE* 5.0 4.3 - - + -
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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