Contacts of the strand formed by residues 5 - 13 (chain A) in PDB entry 1RJJ
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 GLY 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA* 5.1 1.3 - - - -
4A SER* 1.3 85.8 + - - +
6A PHE* 1.3 60.3 + - - -
63A THR* 4.9 6.3 - - - -
64A PHE 3.7 11.2 - - - -
65A GLU* 4.6 2.0 - - - -
99A PRO* 3.7 1.9 - - - +
100A VAL* 2.7 41.7 + - - +
102A ALA* 5.2 1.2 - - - +
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Residues in contact with PHE 6 (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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1A MET 5.5 2.5 - - - -
2A ALA* 4.4 24.0 - - + -
4A SER 3.7 2.4 + - - +
5A GLY* 1.3 73.7 - - - -
7A LYS* 1.3 60.6 + - - +
63A THR* 3.2 6.4 - - - +
64A PHE* 3.0 56.3 + + + +
66A ASN* 5.1 9.4 - - - +
67A LYS* 5.5 3.4 - - + +
70A TYR* 4.4 22.4 - + + -
97A ASP* 2.6 44.6 - - + -
98A PHE* 4.1 15.0 - - - -
99A PRO* 4.2 10.5 - - + -
47B GLU 5.9 1.6 - - - -
48B SER* 6.3 1.3 - - - -
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Residues in contact with LYS 7 (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 GLY 4.1 0.4 + - - -
6A PHE* 1.3 76.2 - - - +
8A HIS* 1.3 59.0 + - - +
9A LEU* 3.0 45.9 - - - +
61A SER* 3.9 15.9 - - - -
62A MET 3.6 2.2 - - - +
63A THR* 3.4 21.8 - - + +
97A ASP* 2.4 40.6 - - - +
98A PHE* 3.2 31.7 + - + +
100A VAL* 3.8 19.7 - - + -
7B LYS* 5.8 1.4 - - - +
9B LEU* 5.4 4.4 - - - +
44B GLU* 3.6 18.2 - - - +
61B SER* 5.1 7.0 - - - +
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Residues in contact with HIS 8 (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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7A LYS* 1.3 77.3 + - - +
9A LEU* 1.3 68.1 + - - +
10A VAL* 5.1 2.5 - - + -
60A PHE 3.6 0.9 - - - +
61A SER* 3.9 1.2 - - - -
62A MET* 2.8 57.1 + - + +
64A PHE* 4.5 10.5 - - + -
70A TYR* 5.5 7.7 - + + -
95A LEU* 3.3 41.5 - - + +
96A LEU 3.8 1.6 - - - -
97A ASP* 2.9 34.6 + - + +
52B LEU* 5.3 13.2 - - + -
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Residues in contact with LEU 9 (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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7A LYS* 3.0 31.2 - - - +
8A HIS* 1.3 79.9 - - - +
10A VAL* 1.3 78.6 + - - +
11A VAL* 3.5 18.4 - - + -
44A GLU* 5.1 3.8 - - - +
59A ALA* 4.2 9.4 - - + -
60A PHE 3.5 9.6 - - - +
61A SER* 3.9 14.4 - - - +
95A LEU* 2.9 27.1 - - - +
96A LEU* 3.0 40.4 + - + +
98A PHE* 5.4 0.2 - - + -
7B LYS* 5.4 4.3 - - - +
9B LEU* 4.8 15.9 - - + -
96B LEU* 6.2 2.5 - - + -
98B PHE* 6.1 1.8 - - + -
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Residues in contact with VAL 10 (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 HIS* 5.4 2.9 - - + -
9A LEU* 1.3 78.3 - - - +
11A VAL* 1.3 65.0 + - - +
12A VAL* 3.5 9.4 - - + -
59A ALA* 2.8 27.3 - - - +
60A PHE* 3.4 41.8 + - + +
62A MET* 5.3 4.3 - - + -
86A PHE* 4.1 9.0 - - + -
93A ILE* 3.4 35.0 - - + -
94A VAL 3.1 8.7 - - - +
95A LEU* 4.0 12.1 - - + -
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Residues in contact with VAL 11 (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* 3.5 18.6 - - + -
10A VAL* 1.3 75.7 - - - +
12A VAL* 1.3 68.2 + - - +
46A LYS* 4.6 2.7 - - - -
56A PHE* 3.2 46.4 - - + -
58A HIS 4.1 1.3 - - - -
59A ALA* 4.6 8.1 - - + -
92A LYS 3.9 0.3 - - - +
94A VAL* 2.7 47.0 + - + +
96A LEU* 4.1 11.0 - - + -
96B LEU* 3.9 24.9 - - + -
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Residues in contact with VAL 12 (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 VAL* 3.5 25.6 - - + -
11A VAL* 1.3 82.2 - - - +
13A LYS* 1.3 61.2 + - - +
18A THR* 6.0 0.9 - - + -
56A PHE* 3.3 9.7 - - - +
57A THR* 3.2 37.9 + - + +
58A HIS* 3.3 24.6 + - + +
60A PHE* 5.6 0.9 - - + -
86A PHE* 4.2 11.7 - - + -
90A ILE* 3.4 25.4 - - + -
92A LYS* 3.4 17.3 - - - +
93A ILE* 3.8 10.3 - - + -
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Residues in contact with LYS 13 (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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12A VAL* 1.3 76.0 - - - +
14A PHE* 1.3 108.5 + - - +
55A GLY 3.1 20.6 - - - +
56A PHE* 3.1 25.5 + - - +
57A THR* 3.9 4.5 - - - -
90A ILE* 3.7 5.5 - - - +
91A ASP* 2.8 34.7 + - + +
92A LYS* 3.4 29.3 - - + +
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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