Contacts of the strand formed by residues 30 - 35 (chain A) in PDB entry 3RLG
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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8A TRP* 3.8 12.0 - - - +
9A ILE 3.0 15.8 + - - -
10A MET* 3.2 17.4 - - - +
11A GLY 2.8 20.5 + - - -
28A ALA* 3.4 6.9 - - - +
29A ASN* 1.3 86.6 + - - +
31A ILE* 1.4 68.2 + - - +
85A LEU* 3.6 4.1 - - - +
87A LEU* 3.0 37.5 - - - -
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Residues in contact with ILE 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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10A MET* 3.6 7.1 - - - +
11A GLY 3.5 7.0 - - - +
14A VAL* 3.8 31.0 - - + -
20A ILE* 4.2 7.9 - - + -
23A PHE* 4.7 10.3 - - + -
24A VAL* 4.7 8.3 - - + -
30A SER* 1.4 81.2 - - - +
32A GLU* 1.3 60.2 + - - +
33A THR* 3.6 19.5 - - - +
66A PHE* 3.9 18.8 - - + -
70A LEU* 4.0 19.3 - - + -
85A LEU* 4.1 12.6 - - + -
87A LEU 3.1 3.8 + - - +
88A VAL* 3.3 17.8 - - + -
89A VAL 2.8 24.3 + - - -
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Residues in contact with GLU 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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10A MET* 4.0 5.6 - - - -
11A GLY 2.7 14.6 + - - +
12A ALA* 3.9 2.1 - - - +
13A MET* 2.9 32.1 + - - +
14A VAL* 2.8 32.1 + - - +
31A ILE* 1.3 73.6 - - - +
33A THR* 1.3 61.3 + - - +
34A ASP* 4.1 2.9 - - - +
89A VAL* 3.2 22.4 - - + +
91A ASP* 3.2 14.1 - - + +
250A MET* 3.8 34.1 - - + +
286A MG 2.2 31.7 - - - -
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Residues in contact with THR 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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14A VAL 2.8 23.4 + - - +
15A ASN* 3.4 8.1 - - - +
31A ILE* 3.6 10.2 - - - +
32A GLU* 1.3 76.7 - - - +
34A ASP* 1.3 66.4 + - - +
35A VAL* 4.1 0.5 - - - +
45A THR* 3.6 28.0 - - + -
66A PHE* 3.4 23.0 - - + -
88A VAL* 4.4 1.4 - - - +
89A VAL 2.9 6.4 + - - -
90A PHE* 3.4 25.1 - - + -
91A ASP* 2.8 26.4 + - - -
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Residues in contact with ASP 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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13A MET* 3.4 9.9 - - - +
15A ASN* 2.9 32.8 + - - +
32A GLU* 3.3 2.6 - - - +
33A THR* 1.3 72.8 - - - +
35A VAL* 1.3 63.1 + - - +
36A SER 4.1 0.4 - - - -
45A THR* 2.9 30.2 - - - +
46A TYR 3.8 16.2 - - - +
47A HIS* 3.3 23.7 - - - -
91A ASP* 3.1 11.3 - - - +
93A LYS* 3.2 9.6 - - - -
286A MG 2.2 30.7 - - - -
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Residues in contact with VAL 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 THR* 4.1 0.9 - - + +
34A ASP* 1.3 79.9 - - - +
36A SER* 1.3 71.0 + - - +
37A PHE* 3.6 13.3 - - + -
42A PRO* 3.7 22.9 - - + -
44A TYR 3.6 2.9 - - - +
45A THR* 4.6 0.2 - - - +
63A PHE* 3.6 22.9 - - + -
90A PHE* 3.6 40.8 - - + -
91A ASP 2.9 8.4 + - - +
92A LEU* 4.0 11.9 - - + -
93A LYS* 2.8 32.6 + - - +
109A LEU* 4.2 3.6 - - + -
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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