Contacts of the strand formed by residues 30 - 38 (chain A) in PDB entry 6BCH
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 SER 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ALA* 2.6 35.2 + - - +
28A ALA 3.8 0.2 - - - -
29A ASP* 1.3 80.4 - - - +
31A SER* 1.3 57.4 + - - +
32A PHE* 4.4 0.2 - - - -
52A PHE* 3.6 16.8 - - - -
53A ARG 3.4 13.5 - - - -
54A ILE* 3.6 19.5 - - - -
108A LYS* 2.5 42.3 + - - +
17X A 4.8 0.2 - - - +
18X G 3.4 5.8 + - - -
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Residues in contact with SER 31 (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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29A ASP 5.3 0.2 - - - -
30A SER* 1.3 75.6 - - - +
32A PHE* 1.3 66.7 + - - +
33A MET* 3.6 29.7 + - - +
51A ARG 3.9 0.3 - - - +
52A PHE* 3.5 5.7 - - - -
53A ARG* 2.9 41.9 + - - -
108A LYS* 4.5 1.6 - - - +
144A ASN* 3.8 5.7 + - - -
17X A 4.7 8.3 - - - -
18X G 3.7 29.7 + - - -
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Residues in contact with PHE 32 (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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30A SER* 4.4 0.7 - - - -
31A SER* 1.3 72.2 + - - +
33A MET* 1.3 56.8 + - - +
51A ARG 3.6 2.5 - - - -
52A PHE* 3.3 36.6 - + + -
95A VAL* 4.5 2.5 - - + -
99A PHE* 3.7 14.1 - + - -
104A LEU* 3.7 12.3 - - + -
108A LYS* 3.7 35.8 - - + +
111A ASP* 4.8 3.6 - - + +
112A TYR* 3.4 42.2 - + + -
115A PHE* 3.6 40.8 - + + -
143A LEU* 3.8 13.8 - - + +
144A ASN* 2.5 35.8 + - - +
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Residues in contact with MET 33 (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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31A SER* 3.6 22.4 - - - +
32A PHE* 1.3 77.3 - - - +
34A LEU* 1.3 67.4 + - - +
35A THR* 4.2 1.6 - - - +
50A PRO* 3.5 4.0 - - - +
51A ARG* 2.9 59.8 + - + +
53A ARG* 3.6 47.6 - - + +
115A PHE* 3.6 3.8 - - - -
143A LEU* 4.1 3.4 - - - -
144A ASN* 4.2 1.3 - - - +
18X G 4.3 4.9 - - + -
19X G 3.5 51.1 - - - +
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Residues in contact with LEU 34 (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 MET* 1.3 82.4 - - - +
35A THR* 1.3 62.0 + - - +
36A VAL* 5.4 1.1 - - + -
48A VAL* 5.1 5.2 - - + -
49A ARG 3.4 3.4 - - - +
50A PRO* 3.8 24.5 - - + -
114A LEU 5.4 0.2 - - - -
115A PHE* 4.5 10.1 - - + +
118A ALA* 3.6 34.5 - - + -
122A ILE* 4.3 7.0 - - + -
136A ILE* 4.4 10.5 - - + +
139A LEU* 4.7 3.1 - - + -
140A LYS* 2.7 63.9 + - + +
143A LEU* 3.7 25.2 - - + +
19X G 5.2 1.4 + - - -
20X A 4.7 0.7 + - - -
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Residues in contact with THR 35 (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 MET* 4.2 1.6 - - - +
34A LEU* 1.3 72.3 - - - +
36A VAL* 1.3 64.0 + - - +
37A SER* 3.6 22.7 - - - +
47A SER* 3.3 2.0 - - - +
48A VAL* 3.2 5.9 - - - +
49A ARG* 2.9 46.1 + - + +
51A ARG* 2.8 44.1 + - - +
140A LYS* 5.0 0.4 - - - +
20X A 4.2 23.5 + - + +
21X G 4.3 7.2 - - - +
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.9 2.8 + - + +
35A THR* 1.3 76.7 - - - +
37A SER* 1.3 59.9 + - - +
46A TRP* 3.6 34.0 - - + -
47A SER 3.2 6.7 - - - +
48A VAL* 3.6 26.7 - - + -
133A LEU* 4.6 0.2 - - + -
136A ILE* 4.9 4.7 - - + -
137A LEU* 4.3 21.8 - - + -
140A LYS* 4.0 23.4 - - + +
151A LEU* 3.9 28.1 - - + +
155A PHE* 5.1 0.9 - - + -
20X A 5.4 1.8 + - - -
21X G 5.0 2.8 + - - -
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Residues in contact with SER 37 (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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35A THR* 3.6 19.5 - - - +
36A VAL* 1.3 71.6 + - - +
38A LYS* 1.3 67.0 + - - +
46A TRP* 3.4 5.5 - - - -
47A SER* 2.8 46.4 + - - -
20X A 4.4 0.7 - - - +
21X G 3.6 39.6 + - - -
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Residues in contact with LYS 38 (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* 1.3 75.2 - - - +
39A ASP* 1.3 60.6 + - - +
40A SER 4.4 0.2 - - - -
45A GLY 3.7 3.8 - - - +
46A TRP* 3.2 31.9 - - + -
21X G 5.3 1.2 + - - -
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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