Contacts of the strand formed by residues 92 - 99 (chain Q) in PDB entry 2A3W
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 92 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q PHE 4.1 0.3 - - - +
38Q ARG* 3.3 7.7 - - - +
39Q ALA* 2.8 49.4 + - + +
65Q LYS* 6.1 0.7 - - - +
71Q TYR* 3.6 21.8 - - - +
86Q GLU* 4.3 5.6 - - - +
90Q ALA 4.3 5.4 - - - +
91Q PRO* 1.3 75.6 - - - +
93Q HIS* 1.3 66.8 + - - +
94Q ILE* 3.7 24.2 - - + +
109Q ILE* 3.7 25.1 - - + -
110Q ASN* 3.6 10.1 - - - +
203Q TRP* 4.7 0.8 - - - -
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Residues in contact with HIS 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Q CYS* 4.1 12.3 - - + +
37Q PHE* 3.6 19.3 + - - -
38Q ARG* 3.8 31.4 - - + +
92Q VAL* 1.3 73.7 - - - +
94Q ILE* 1.3 61.4 + - - +
95Q CYS* 3.4 31.6 + - - -
108Q TRP 3.5 1.5 + - - +
109Q ILE* 3.4 5.4 - - - -
110Q ASN* 2.8 38.4 + - - +
111Q GLY 4.8 3.8 + - - -
156Q ASP* 5.2 4.2 + - + +
169Q ILE* 4.4 0.9 - - + +
172Q ALA* 3.9 11.6 + - + +
173Q TYR* 3.5 53.7 - + + +
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Residues in contact with ILE 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q LEU 3.8 0.7 - - - +
36Q CYS* 3.1 2.9 - - - -
37Q PHE* 2.8 77.8 + - + +
39Q ALA* 4.7 3.8 - - + -
49Q LEU* 4.1 9.4 - - + -
63Q VAL* 5.1 1.8 - - + -
71Q TYR* 3.6 23.1 - - + -
92Q VAL* 3.7 24.7 - - + -
93Q HIS* 1.3 79.5 - - - +
95Q CYS* 1.3 73.2 + - - +
96Q VAL* 4.8 1.1 - - + +
107Q PHE* 4.3 16.4 - - + -
108Q TRP 3.4 2.7 - - - -
109Q ILE* 3.8 23.8 - - + -
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Residues in contact with CYS 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q THR* 4.9 0.4 - - + -
35Q LEU 3.1 3.8 - - - -
36Q CYS* 2.0 45.5 - - - -
93Q HIS* 3.4 20.4 - - - -
94Q ILE* 1.3 74.8 - - - +
96Q VAL* 1.3 60.7 + - - +
106Q GLU 4.3 0.4 - - - -
107Q PHE* 3.4 5.5 - - - -
108Q TRP* 2.7 47.0 + - + +
169Q ILE* 3.8 33.9 - - + -
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Residues in contact with VAL 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q PHE* 4.0 6.5 - - + -
34Q THR* 3.3 2.6 - - - -
35Q LEU* 2.7 56.1 + - + +
37Q PHE* 5.5 0.4 - - + -
63Q VAL* 3.8 28.7 - - + -
73Q LEU* 4.0 20.9 - - + -
94Q ILE* 5.5 2.0 - - + -
95Q CYS* 1.3 75.4 - - - +
97Q SER* 1.3 68.9 + - - +
105Q ALA* 5.2 0.2 - - + -
106Q GLU 3.2 11.7 - - - +
107Q PHE* 3.7 35.9 - - + -
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Residues in contact with SER 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q PHE* 3.1 15.3 - - - -
34Q THR* 3.4 19.7 - - - -
96Q VAL* 1.3 77.9 - - - +
98Q TRP* 1.3 62.8 + - - +
104Q ILE 4.4 1.1 + - - -
105Q ALA* 3.3 5.9 - - - +
106Q GLU* 3.0 50.4 + - - +
108Q TRP* 5.5 1.7 + - - -
163Q VAL* 3.5 24.3 - - - +
164Q LEU 4.7 2.5 + - - -
169Q ILE* 5.7 2.0 - - - -
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Residues in contact with TRP 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Q LEU 4.2 0.2 - - - -
31Q GLN 3.5 18.2 - - - -
32Q ASN* 3.4 5.4 - - - -
33Q PHE* 3.0 62.3 + + + +
73Q LEU* 4.1 5.8 - - + -
75Q ILE* 3.8 29.2 - - + -
97Q SER* 1.3 76.5 - - - +
99Q GLU* 1.3 66.6 + - - +
100Q SER* 3.7 10.5 - - - -
103Q GLY 3.3 18.0 + - - -
104Q ILE 3.4 7.4 - - - -
105Q ALA* 4.3 2.0 - - + -
119Q LEU* 3.1 37.3 + - + +
120Q ARG 3.3 23.1 - - - -
123Q TYR* 3.3 28.9 - + - -
125Q VAL* 3.7 21.1 - - + -
163Q VAL* 3.8 4.1 - - - +
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Residues in contact with GLU 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199P LYS* 2.7 29.6 + - - -
32Q ASN* 3.7 15.3 - - - +
98Q TRP* 1.3 79.7 - - - +
100Q SER* 1.3 54.8 + - - +
101Q SER* 3.4 21.8 + - - +
102Q SER* 2.6 26.8 + - - +
103Q GLY* 2.7 36.7 + - - -
104Q ILE* 3.1 11.8 + - + +
163Q VAL* 3.8 23.0 - - + +
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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
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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