Contacts of the strand formed by residues 34 - 41 (chain B) in PDB entry 3Q3G
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 ILE 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B PHE* 3.6 29.2 - - + -
30B ASN 4.0 8.1 - - - +
31B ILE* 3.3 16.6 - - - +
32B LYS 3.4 1.8 - - - +
33B ASP* 1.3 84.9 - - + +
35B TYR* 1.3 64.7 + - - +
36B MET* 3.7 27.8 - - + +
54B ASP* 4.2 3.8 - - - +
55B PRO* 3.4 18.4 - - - +
100B SER* 3.4 29.8 - - - +
101B GLU 3.7 6.7 - - - +
102B GLY* 3.9 18.4 - - - -
103B HIS* 3.6 14.5 - - - -
104B TYR* 5.7 1.6 - - - +
113B TYR* 6.2 0.9 - - + -
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Residues in contact with TYR 35 (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 TYR* 4.4 0.7 - - - -
34B ILE* 1.3 79.5 - - - +
36B MET* 1.3 61.7 + - - +
37B GLN* 3.6 16.5 + - - +
52B ARG* 3.9 20.4 + - - -
53B ILE 3.4 3.4 - - - -
54B ASP* 3.6 38.8 + - + -
100B SER* 3.4 4.3 - - - -
101B GLU* 2.9 56.4 + - - +
103B HIS* 3.5 26.2 - + - -
177E SER* 4.7 0.2 + - - -
178E GLU* 3.5 36.8 - - - +
179E GLU* 4.9 3.2 - - + +
205E LEU* 3.8 3.1 + - - +
206E LEU 3.2 24.9 + - - -
207E GLY* 4.2 5.8 - - - -
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Residues in contact with MET 36 (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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6B LEU* 4.1 13.5 - - + -
24B CYS* 4.0 17.7 - - - +
26B PRO* 3.8 17.7 - - + -
31B ILE* 3.6 30.5 - - + -
34B ILE* 3.7 18.2 - - + +
35B TYR* 1.3 71.7 - - - +
37B GLN* 1.3 67.3 + - - +
38B TRP* 4.5 6.7 - - - +
52B ARG* 3.1 3.4 - - - -
53B ILE* 2.9 53.4 + - + +
55B PRO* 4.5 5.8 - - + +
81B ALA* 3.6 24.2 - - + -
98B CYS* 4.6 5.4 - - + -
99B ALA 3.8 12.6 - - - +
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Residues in contact with GLN 37 (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 TYR* 5.2 0.2 + - - -
102A LEU* 3.5 13.0 - - - +
35B TYR* 3.6 18.2 - - - +
36B MET* 1.3 74.0 - - - +
38B TRP* 1.3 65.0 + - - +
39B VAL* 4.2 1.1 - - + -
49B TRP* 2.8 27.1 + - + +
51B GLY 3.5 4.0 - - - -
52B ARG* 3.2 18.1 - - - +
98B CYS* 3.1 9.0 - - - +
99B ALA* 2.6 44.9 + - + +
101B GLU* 3.2 37.8 + - - +
111B MET* 4.1 26.5 - - + -
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Residues in contact with TRP 38 (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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8B GLN* 3.8 20.9 - - - -
22B LEU* 4.1 18.4 - - + -
23B SER 4.1 9.9 - - - -
24B CYS* 3.8 31.0 - - + -
36B MET* 4.5 5.1 - - - +
37B GLN* 1.3 79.4 + - - +
39B VAL* 1.3 58.9 + - - +
49B TRP* 3.9 1.7 - - - -
50B ILE* 2.8 49.1 + - + +
51B GLY 3.0 12.2 + - - +
72B ILE* 3.6 34.4 - - + +
81B ALA* 3.8 19.0 - - + +
82B TYR 3.5 14.3 + - - +
83B LEU* 3.5 38.1 - - + -
96B TYR* 4.5 8.5 - + + -
97B TYR 3.4 18.6 - - - -
98B CYS* 3.9 7.6 - - + -
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Residues in contact with VAL 39 (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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104A PHE* 4.2 11.9 - - + -
37B GLN* 4.8 1.3 - - + -
38B TRP* 1.3 80.5 - - - +
40B LYS* 1.3 61.0 + - - +
47B LEU* 3.8 28.5 - - + -
48B GLU 3.5 24.9 - - - +
49B TRP* 4.3 8.5 - - + -
50B ILE* 4.4 3.6 - - - -
95B VAL 3.9 0.3 - - - +
96B TYR* 3.5 2.3 - - - -
97B TYR* 2.8 41.0 + - + +
99B ALA* 5.0 1.6 - - + -
111B MET* 4.1 17.5 - - - -
114B TRP* 4.0 27.8 - - + -
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Residues in contact with LYS 40 (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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39B VAL* 1.3 72.8 - - - +
41B GLN* 1.3 63.5 + - - +
42B ARG* 3.7 26.6 + - - +
46B GLY 3.6 2.6 - - - +
47B LEU* 3.6 2.3 - - - -
48B GLU* 2.7 63.2 + - + +
50B ILE* 4.0 7.7 - - + +
66B PHE* 3.9 25.3 - - + -
91B GLU* 3.0 30.4 + - - +
92B ASP* 4.3 7.3 + - - -
94B ALA* 3.7 12.1 - - + -
95B VAL 3.7 3.6 - - - -
96B TYR* 3.6 36.1 - - + +
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Residues in contact with GLN 41 (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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44A GLN* 2.9 43.0 + - - +
93A TYR* 3.4 13.9 + - - -
618A EDO 4.0 12.4 - - - -
40B LYS* 1.3 73.7 - - - +
42B ARG* 1.3 64.0 + - - +
43B PRO* 3.9 0.7 - - - +
45B GLN 3.7 14.9 - - - +
46B GLY 3.8 5.2 - - - +
47B LEU* 3.5 16.9 - - + +
94B ALA* 3.7 3.3 - - - -
95B VAL* 2.8 44.8 + - + +
97B TYR* 3.4 25.6 + - + -
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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