Contacts of the strand formed by residues 30 - 38 (chain D) in PDB entry 2BNQ
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 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D PHE* 3.7 28.5 - - + -
27D ASP* 3.4 22.2 - - + +
28D SER 2.8 15.4 + - - +
29D ALA* 1.3 75.2 - - - +
31D TYR* 1.3 59.3 + - - +
32D ASN 3.9 20.2 - - - +
33D LEU* 4.5 0.7 - - + -
52D SER* 2.9 23.0 - - - -
66D LEU* 4.3 17.9 - - + -
68D LYS* 4.1 10.5 - - + +
92D VAL* 3.8 31.4 - - + -
93D ARG 3.2 11.4 - - - +
94D PRO* 5.2 0.7 - - + -
95D THR* 2.8 15.2 - - - +
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Residues in contact with TYR 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLN* 3.5 43.3 - - + +
5C TRP* 3.4 78.8 + + + +
7C THR* 4.5 2.6 + - - -
30D ILE* 1.3 75.2 - - - +
32D ASN* 1.3 70.6 + - - +
51D GLN* 3.8 3.9 - - - +
52D SER* 2.9 22.4 + - - -
93D ARG* 2.7 15.7 + - + +
94D PRO 3.9 2.0 - - - +
95D THR* 3.4 7.2 - - + +
96E GLY* 3.6 2.1 - - - -
97E ASN* 2.6 38.3 + - - -
98E THR 3.8 11.9 - - - -
99E GLY 4.0 0.4 - - - -
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Residues in contact with ASN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 3.5 9.2 - - - +
31D TYR* 1.3 85.3 - - - +
33D LEU* 1.3 67.5 + - - +
34D GLN* 4.5 3.5 + - - +
49D LEU* 3.9 18.6 - - + +
50D ILE 3.3 14.4 - - - +
51D GLN* 4.1 1.8 - - - -
52D SER* 4.0 4.3 - - - +
91D ALA 4.7 0.3 - - - +
92D VAL* 3.4 6.9 - - - +
93D ARG* 3.4 38.8 + - - +
98E THR 2.9 27.8 + - - +
99E GLY* 3.2 24.0 + - - -
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PHE* 3.4 32.5 - - + -
30D ILE* 4.5 1.3 - - + -
32D ASN* 1.3 78.4 - - - +
34D GLN* 1.3 62.9 + - - +
35D TRP* 3.4 35.4 - - + +
48D LEU 4.1 0.5 - - - +
49D LEU* 3.6 2.1 - - - +
50D ILE* 2.8 48.7 + - + +
66D LEU* 3.9 9.2 - - + -
73D SER* 3.5 22.2 - - - +
90D CYS* 3.8 16.2 - - - -
91D ALA 3.3 9.9 - - - +
92D VAL* 3.6 12.1 - - + -
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Residues in contact with GLN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ASN* 4.5 3.3 + - - +
33D LEU* 1.3 76.6 - - - +
35D TRP* 1.3 65.4 + - - +
36D PHE* 3.2 27.6 - - + -
46D SER* 2.8 24.9 + - - +
48D LEU 3.4 15.3 - - - +
49D LEU* 3.6 18.5 - - + +
89D LEU 3.8 0.7 - - - +
90D CYS* 3.5 2.6 - - - -
91D ALA* 2.8 40.0 + - + +
99E GLY 4.7 0.5 - - - +
100E GLU* 3.4 8.1 - - - +
101E LEU* 2.9 52.2 + - - +
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Residues in contact with TRP 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLN* 3.7 19.3 - - - -
21D LEU* 4.0 17.9 - - + -
22D ASN 4.0 11.9 - - - -
23D CYS* 3.6 29.6 - - + -
33D LEU* 3.4 18.5 - - + +
34D GLN* 1.3 75.1 - - - +
36D PHE* 1.3 63.5 + - - +
46D SER* 3.8 2.6 + - - -
47D LEU* 2.8 28.4 + - + -
48D LEU* 2.9 25.2 + - + +
50D ILE* 5.8 1.3 - - + -
64D ALA* 4.1 20.0 - - + +
73D SER* 3.2 22.6 + - - -
75D LEU* 3.6 55.7 - - + +
88D TYR* 4.3 10.3 - - + -
89D LEU 3.4 17.5 - - - -
90D CYS* 4.1 8.1 - - + -
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Residues in contact with PHE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLN* 3.2 54.3 - - + -
35D TRP* 1.3 75.8 - - - +
37D ARG* 1.3 64.0 + - - +
44D LEU* 4.4 14.1 - - + -
45D THR 3.2 10.1 - - - +
46D SER* 3.7 21.5 - - - -
47D LEU* 3.6 9.2 - - - +
88D TYR* 3.3 6.4 - - - +
89D LEU* 2.8 44.7 + - + +
91D ALA* 4.2 5.2 - - + -
104D PHE* 3.8 25.6 - + - -
101E LEU* 4.2 8.3 - - + -
103E PHE* 3.7 35.7 - + - -
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Residues in contact with ARG 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D PHE* 1.3 76.2 - - - +
38D GLN* 1.3 60.9 + - - +
39D ASP* 2.9 34.8 + - - -
42D LYS* 4.9 4.9 + - - +
43D GLY 3.9 0.7 - - - +
44D LEU* 3.6 1.4 - - - -
45D THR* 2.9 47.7 + - - +
47D LEU* 3.6 32.1 - - + -
83D GLY 3.0 30.1 + - - -
84D ASP* 3.9 12.7 + - - +
85D SER 3.4 7.9 + - - -
86D ALA* 3.9 9.6 - - + +
87D THR 3.2 7.6 - - - +
88D TYR* 3.9 20.8 + - + -
89D LEU* 5.9 0.2 - - - -
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Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ARG* 1.3 74.7 - - - +
39D ASP* 1.3 75.9 + - - +
40D PRO* 4.2 1.7 - - + +
41D GLY 5.8 0.2 + - - -
42D LYS* 3.1 15.7 - - - +
43D GLY 3.2 16.4 - - - +
44D LEU* 3.4 26.3 - - + +
86D ALA* 3.5 0.6 - - - +
87D THR* 2.8 45.9 + - - +
89D LEU* 4.1 8.3 - - + +
36E GLN* 2.9 43.7 + - - -
89E PHE* 3.9 6.4 - - - -
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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