Contacts of the strand formed by residues 51 - 57 (chain B) in PDB entry 1J7D
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 THR 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B LYS* 5.3 5.6 - - - +
38B VAL* 3.9 19.7 - - + -
39B ILE 3.6 4.3 - - - -
40B ALA* 4.9 9.0 - - + -
49B GLY 5.0 3.4 - - - +
50B GLY* 1.3 77.0 - - - +
52B PHE* 1.3 63.8 + - - +
53B LYS* 4.2 2.6 + - - +
73B THR* 4.3 3.8 + - - +
148B ALA* 2.8 27.0 + - - +
149B MET 5.2 0.7 - - - -
150B ASN 4.1 15.1 + - - -
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 3.3 4.7 - - - -
39B ILE* 2.8 49.1 + - + +
41B GLY* 4.0 6.1 - - - -
47B PHE* 3.7 37.0 - + + -
50B GLY 3.8 18.4 - - - -
51B THR* 1.3 74.1 - - - +
53B LYS* 1.3 64.2 + - - +
54B LEU* 3.3 4.1 - - + +
71B PHE* 3.8 23.8 - + + -
73B THR* 3.8 18.2 - - + -
74B LYS 4.5 4.3 - - - -
75B ILE* 3.7 35.2 - - + -
112B LEU* 4.6 6.7 - - + -
144B THR* 3.8 13.2 - - + -
148B ALA* 3.6 20.4 - - + -
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Residues in contact with LYS 53 (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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37B VAL 3.4 6.3 - - - +
38B VAL* 4.6 13.5 - - + +
51B THR 5.4 2.2 - - - +
52B PHE* 1.3 72.7 - - - +
54B LEU* 1.3 61.0 - - - +
71B PHE* 3.5 3.5 - - - -
72B MET* 2.8 44.1 + - + +
73B THR* 2.8 22.6 + - - +
150B ASN 5.8 7.8 - - - -
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Residues in contact with LEU 54 (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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36B HIS* 3.8 2.4 + - - -
37B VAL* 2.7 42.7 + - + +
39B ILE* 3.5 34.1 - - + -
52B PHE 3.3 24.7 - - - +
53B LYS* 1.3 75.2 - - - +
55B GLU* 1.3 62.2 + - - +
69B VAL* 3.8 25.4 - - + -
70B ARG 3.3 7.0 - - - +
71B PHE* 3.3 49.6 - - + -
72B MET* 4.3 3.8 - - - +
86B ILE* 4.0 3.1 - - + -
105B LEU* 6.1 1.1 - - + -
108B ILE* 3.9 8.1 - - + -
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Residues in contact with GLU 55 (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 ASN* 2.7 22.6 + - - +
13A PHE* 3.5 18.6 - - + -
34B TYR* 2.6 41.1 + - + +
35B PHE 3.4 4.7 - - - +
36B HIS* 4.9 4.7 - - - +
54B LEU* 1.3 75.7 - - - +
56B LEU* 1.3 59.1 + - - +
69B VAL* 3.3 8.8 - - - +
70B ARG* 2.7 75.0 + - + +
72B MET* 3.0 14.3 - - + +
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Residues in contact with LEU 56 (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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13A PHE* 4.3 1.8 - - - -
33B ARG 3.7 0.9 - - - +
34B TYR* 3.5 4.9 - - - -
35B PHE* 2.7 57.2 + - + +
37B VAL* 4.6 8.1 - - + -
55B GLU* 1.3 75.8 - - - +
57B PHE* 1.3 66.6 + - - +
58B LEU* 3.4 35.0 - - + -
67B PRO* 4.1 5.6 - - + -
68B LYS 3.2 3.6 - - - +
69B VAL* 3.8 23.1 - - + -
101B ILE* 3.4 29.8 - - + +
104B VAL* 5.3 2.0 - - + -
105B LEU* 3.6 20.6 - - + -
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Residues in contact with PHE 57 (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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7A VAL* 3.9 16.2 - - + -
8A LYS 3.2 28.0 - - - -
9A VAL* 3.8 18.4 - - + -
10A PRO* 3.3 28.5 - - + -
13A PHE* 3.6 27.1 - + + -
31B ASN* 4.3 2.2 - - - -
33B ARG* 3.3 21.5 - - + -
34B TYR* 4.5 0.4 - - - -
56B LEU* 1.3 76.3 - - - +
58B LEU* 1.3 75.2 + - - +
59B PRO* 3.3 22.6 - - + +
67B PRO* 3.5 2.3 - - - +
68B LYS* 2.8 52.5 + - + +
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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