Contacts of the strand formed by residues 84 - 89 (chain A) in PDB entry 2AQ5
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 VAL 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A SER* 4.9 2.9 + - - -
33A THR* 5.1 1.2 + - - -
39A PHE* 5.2 2.1 - - - -
50A ILE* 3.3 35.3 - - + +
51A CME 5.8 0.8 + - - -
57A GLY* 4.0 5.2 - - - -
58A ALA 3.7 29.1 - - - +
59A PHE* 4.4 7.0 - - + -
80A HIS* 3.6 27.1 - - + -
83A PRO* 1.3 76.0 - - - +
85A LEU* 1.3 67.2 + - - +
86A ASP 3.9 15.0 - - - +
87A ILE* 3.9 17.7 - - + -
99A SER* 4.1 5.8 - - - -
100A GLY 3.6 12.8 - - - +
101A SER* 4.1 0.9 - - - +
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Residues in contact with LEU 85 (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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33A THR* 3.7 30.5 - - + +
35A TRP* 3.4 23.2 - - + +
37A SER* 2.6 28.8 + - - -
39A PHE* 3.8 3.4 - - + -
50A ILE* 3.6 8.1 - - - +
83A PRO 4.1 2.0 - - - +
84A VAL* 1.3 78.4 - - - +
86A ASP* 1.3 53.6 + - - +
100A GLY 2.8 9.7 + - - -
102A GLU* 3.8 23.3 - - + +
133A ARG* 3.7 42.4 - - + +
134A VAL 3.6 22.0 - - - +
135A GLY* 3.8 14.1 - - - -
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Residues in contact with ASP 86 (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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37A SER* 3.5 18.4 - - - -
38A GLY 4.6 2.8 + - - -
39A PHE 5.2 2.0 + - - +
50A ILE* 3.8 4.6 - - - +
84A VAL* 3.9 0.3 - - - +
85A LEU* 1.3 81.4 - - - +
87A ILE* 1.3 77.4 + - - +
88A ALA* 5.9 0.2 - - - -
99A SER* 3.2 4.5 - - - -
100A GLY 2.8 30.1 + - - +
134A VAL 5.1 0.2 - - - +
135A GLY* 3.4 22.2 - - - +
136A ILE* 3.4 7.4 - - - +
137A VAL* 3.0 38.2 + - + +
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Residues in contact with ILE 87 (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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39A PHE* 4.2 4.7 - - - +
40A CYS 4.7 3.0 - - - +
41A ALA* 3.6 21.8 - - + +
48A ALA* 3.8 42.8 - - + +
49A LEU* 3.9 16.2 - - - +
50A ILE* 4.1 11.0 - - + -
59A PHE* 3.9 24.2 - - + -
84A VAL* 3.9 8.1 - - + -
86A ASP* 1.3 89.5 + - - +
88A ALA* 1.3 64.0 + - - +
97A ILE* 4.0 6.1 - - + -
98A ALA 3.2 6.7 - - - +
99A SER* 3.9 18.8 - - - -
137A VAL* 4.3 2.2 - - - -
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Residues in contact with ALA 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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41A ALA* 4.3 4.5 - - - -
87A ILE* 1.3 77.5 - - - +
89A TRP* 1.3 59.8 + - - +
97A ILE* 3.8 5.3 - - - +
98A ALA 2.9 23.3 + - - -
137A VAL* 3.9 26.7 - - + +
138A ALA* 5.2 1.8 - - - +
139A TRP* 2.9 32.7 + - + -
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Residues in contact with TRP 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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41A ALA* 2.9 41.8 + - + +
42A VAL* 3.6 16.4 - - - +
43A ASN* 3.3 30.1 - - + +
46A PHE* 3.4 37.7 + + + -
48A ALA* 3.9 11.0 - - + -
61A VAL* 3.8 12.8 - - + -
88A ALA* 1.3 72.8 - - - +
90A CSO 1.3 67.5 + - - +
91A PRO* 3.4 4.9 - - - +
94A ASP 3.6 15.0 - - - -
95A ASN 4.0 3.4 - - - -
96A VAL 3.3 31.9 - - - -
97A ILE* 3.6 33.0 - - + +
111A ILE* 4.0 8.5 - - + -
139A TRP* 3.1 11.7 - - - -
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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