Contacts of the strand formed by residues 36 - 41 (chain B) in PDB entry 4J84
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 ARG 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP* 4.8 2.6 + - - -
32A LEU* 6.0 0.8 - - - +
34A SER* 5.9 0.6 + - - -
36A ARG* 3.5 53.0 - - - +
38A GLU* 5.3 1.0 + - - -
52A GLN* 4.2 11.3 + - - -
32B LEU* 2.9 37.0 + - + +
34B SER* 3.3 15.6 + - - +
35B GLY* 1.3 79.0 - - - +
37B VAL* 1.3 69.2 + - - +
38B GLU* 2.7 24.8 + - + +
47B GLU* 2.9 30.9 + - - -
50B SER* 3.1 28.0 + - - -
51B ILE 3.4 15.6 - - - +
52B GLN* 3.6 14.2 + - - +
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Residues in contact with VAL 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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29B LEU* 4.4 4.7 - - + -
30B THR 3.3 9.4 - - - +
31B THR* 3.8 24.7 - - + -
32B LEU* 5.0 0.2 - - - -
36B ARG* 1.3 78.9 - - - +
38B GLU* 1.3 65.8 + - - +
39B ILE* 6.0 1.1 - - + -
49B ARG 6.0 0.2 - - - +
50B SER* 3.3 6.2 - - - -
51B ILE* 2.9 45.4 + - + +
53B VAL* 3.8 27.4 - - + -
58B VAL* 4.1 13.5 - - + -
70B ILE* 4.1 23.6 - - + -
72B VAL* 4.2 5.8 - - + -
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Residues in contact with GLU 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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36A ARG* 5.2 1.7 + - - -
11B ASN* 5.5 0.7 + - - -
13B SER* 4.4 15.1 - - - -
28B VAL 3.6 1.4 - - - +
29B LEU* 3.3 3.4 - - - +
30B THR* 2.8 45.0 + - - +
32B LEU* 4.2 14.6 - - + +
36B ARG* 2.7 37.0 + - + +
37B VAL* 1.3 78.6 - - - +
39B ILE* 1.3 63.1 + - - +
40B TRP* 2.8 32.1 + - - +
47B GLU* 3.5 16.9 - - - +
49B ARG 3.8 4.5 - - - -
50B SER* 4.3 0.2 - - - -
295B PHE* 4.5 2.8 - - - -
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Residues in contact with ILE 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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27B TRP* 3.9 32.1 - - + -
28B VAL 3.4 4.9 - - - +
29B LEU* 3.9 15.3 - - + -
37B VAL* 6.0 1.1 - - + -
38B GLU* 1.3 75.9 - - - +
40B TRP* 1.3 58.3 + - - +
47B GLU* 3.4 5.7 - - - +
48B VAL* 2.7 48.3 + - + -
49B ARG* 2.8 29.5 + - + +
63B PHE* 4.0 10.3 - - + -
70B ILE* 4.0 20.9 - - + -
84B TYR* 3.7 30.7 - - + -
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Residues in contact with TRP 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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12A ARG* 3.7 35.2 - - + -
13A SER* 4.1 3.6 - - - -
9B PHE* 3.7 24.2 - + + -
11B ASN* 3.5 15.9 - - - -
27B TRP* 3.1 6.0 - - - -
28B VAL* 2.8 52.1 + - + +
30B THR* 4.6 2.7 - - + -
38B GLU* 2.8 41.2 + - + +
39B ILE* 1.3 73.2 - - - +
41B ASN* 1.3 60.9 + - - +
42B TYR 3.5 1.0 + - - -
45B GLN 3.7 15.9 - - - -
46B VAL* 3.5 21.3 - - - -
47B GLU* 3.3 39.9 - - + -
48B VAL* 4.3 2.5 - - - -
295B PHE* 3.6 25.7 - + - -
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Residues in contact with ASN 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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26B PRO* 3.3 26.1 - - - +
27B TRP* 4.0 15.3 - - + +
40B TRP* 1.3 72.8 - - - +
42B TYR* 1.3 55.9 + - - +
43B GLU* 2.9 23.0 + - - +
44B THR* 2.9 34.2 + - - +
45B GLN* 2.8 31.4 + - - -
46B VAL 3.0 13.8 + - - +
48B VAL* 3.9 9.5 - - + +
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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