Contacts of the strand formed by residues 39 - 45 (chain A) in PDB entry 5JNT
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 TRP 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A THR* 3.9 3.8 - - - -
6A LYS* 3.2 64.2 - - + +
7A SER* 3.8 12.1 - - - -
8A VAL* 3.9 19.3 - - + -
26A PHE* 3.8 31.2 - + - -
30A VAL* 3.7 23.6 - - + +
35A ILE* 3.5 26.3 - - + +
36A SER 3.0 17.4 + - - +
37A GLU 3.3 1.9 - - - +
38A ASN* 1.4 88.0 + - + +
40A ARG* 1.4 58.7 + - - +
41A VAL* 4.0 16.4 + - + +
87A TYR* 5.3 4.7 - + - -
152A PHE* 4.0 17.0 - + - -
153A LEU* 4.0 17.5 - - + +
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Residues in contact with ARG 40 (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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5A THR* 3.7 10.6 - - + +
6A LYS 2.9 7.0 + - - +
7A SER* 3.1 13.2 - - - -
8A VAL* 2.9 27.3 + - - +
39A TRP* 1.4 71.5 - - - +
41A VAL* 1.3 65.7 + - - +
42A ASP* 5.0 5.8 + - + +
75A ARG* 5.2 1.2 - - - +
81A ASP* 4.5 4.8 + - - -
84A THR* 3.0 40.0 + - - +
85A PHE* 3.3 40.0 - - + -
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Residues in contact with VAL 41 (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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8A VAL* 3.5 4.3 - - + -
10A PHE* 4.0 12.1 - - + -
23A GLU* 3.8 26.6 - - + +
26A PHE* 3.7 39.5 - - + -
27A ARG* 2.9 38.8 + - + +
30A VAL* 4.7 7.0 - - + -
39A TRP* 4.0 16.1 + - + +
40A ARG* 1.3 83.2 - - - +
42A ASP* 1.3 66.4 + - - +
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Residues in contact with ASP 42 (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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8A VAL 3.1 6.5 + - - -
9A LEU* 3.5 12.1 - - + -
10A PHE* 3.0 28.8 + - - -
23A GLU* 3.8 12.9 - - - +
40A ARG* 5.0 5.2 + - + +
41A VAL* 1.3 78.3 - - - +
43A SER* 1.3 80.2 + - - +
72A HIS* 3.6 13.0 + - - -
75A ARG* 2.9 32.7 + - - -
85A PHE* 4.0 13.6 - - + -
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Residues in contact with SER 43 (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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9A LEU* 3.7 3.4 - - - -
10A PHE 3.0 15.0 - - - -
15A ASN* 2.9 22.4 + - - +
19A SER 3.5 22.3 + - - -
20A PRO* 3.8 2.4 - - - +
23A GLU* 2.8 21.9 + - - -
42A ASP* 1.3 84.7 + - - +
44A ALA* 1.4 66.2 + - - +
72A HIS* 3.2 26.9 + - - -
75A ARG* 3.9 4.9 + - - +
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Residues in contact with ALA 44 (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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9A LEU* 3.9 11.4 - - + +
10A PHE 2.9 5.7 + - - +
11A VAL* 3.2 26.9 - - + +
12A CYS 3.3 4.2 + - - -
15A ASN* 3.5 8.9 - - - +
19A SER* 3.6 3.3 + - - -
43A SER* 1.4 77.9 - - - +
45A ALA* 1.3 59.7 + - - +
75A ARG* 3.4 31.2 - - - +
77A ILE* 3.8 22.9 - - + +
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Residues in contact with ALA 45 (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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11A VAL* 4.3 3.6 - - - -
12A CYS 3.2 6.5 - - - -
13A LEU 3.4 11.0 - - - +
14A GLY 3.6 20.9 - - - +
15A ASN* 3.6 2.2 - - + -
44A ALA* 1.3 73.3 - - - +
46A THR* 1.3 63.0 + - - +
47A SER 3.2 20.9 - - - +
51A ILE* 6.0 0.7 - - + -
74A ALA* 5.9 0.2 - - + -
75A ARG 2.8 18.3 + - - +
76A GLN* 3.4 2.0 - - - -
77A ILE* 2.8 26.2 + - - +
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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