Contacts of the strand formed by residues 117 - 125 (chain J) in PDB entry 1N8R
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 LYS 117 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94J ARG* 3.9 2.9 - - - -
95J GLU 3.0 14.2 + - - +
97J LYS* 3.5 50.7 - - + +
116J GLY* 1.3 75.2 - - - -
118J PRO* 1.4 76.7 - - + +
119J VAL* 3.0 14.3 + - + +
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Residues in contact with PRO 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J TYR* 4.9 9.6 - - + +
20J ILE* 4.0 18.6 - - + -
21J SER 4.0 16.6 - - - +
22J GLY 4.0 23.5 - - - +
23J ILE* 4.5 1.8 - - - -
24J PRO* 4.3 9.5 - - + +
92J VAL* 4.1 16.8 - - + -
93J ILE 3.7 7.9 - - - +
94J ARG* 4.3 4.0 - - + -
115J PHE* 6.3 0.7 - - + -
116J GLY 4.4 2.5 - - - +
117J LYS* 1.4 90.7 - - + +
119J VAL* 1.3 61.2 + - - +
120J GLY 3.8 0.4 - - - +
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Residues in contact with VAL 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J TYR* 3.6 26.7 - - + +
24J PRO* 3.6 16.3 - - - +
58J HIS* 5.3 1.9 - - - -
93J ILE* 2.9 20.1 + - + +
94J ARG 3.6 6.1 - - - -
95J GLU* 3.7 25.6 - - + +
97J LYS* 4.0 19.1 - - + +
117J LYS* 3.0 19.1 - - + +
118J PRO* 1.3 74.1 - - - +
120J GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J ILE* 4.7 1.2 - - - +
24J PRO* 4.0 13.2 - - - +
58J HIS* 4.5 9.0 - - - -
92J VAL* 3.6 5.7 - - - +
93J ILE* 2.8 39.1 + - - +
118J PRO 3.8 0.6 - - - -
119J VAL* 1.3 82.6 - - - +
121J THR* 1.3 68.5 + - - +
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Residues in contact with THR 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J ARG* 4.4 7.4 - - - +
23J ILE* 3.6 26.5 - - + -
24J PRO 4.3 9.8 + - - +
26J LYS* 4.9 3.6 - - - +
57J ARG* 3.4 5.0 - - - +
58J HIS* 2.9 42.7 + - - +
89J PRO* 3.7 30.1 - - - +
91J HIS 3.4 7.2 - - - -
92J VAL* 4.4 11.2 - - + +
93J ILE* 3.6 3.6 - - - +
120J GLY* 1.3 78.9 - - - +
122J ALA* 1.3 61.0 + - - +
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Residues in contact with ALA 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J TYR 5.5 0.4 - - - +
55J GLN* 4.3 13.5 - - + +
56J ILE 3.2 26.7 - - - +
57J ARG* 3.6 6.7 - - + +
89J PRO* 3.5 7.6 - - - -
90J PHE 3.2 3.5 + - - -
91J HIS* 2.9 39.0 + - + +
93J ILE* 4.0 16.4 - - + -
121J THR* 1.3 76.0 - - - +
123J ALA* 1.3 59.4 - - - +
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Residues in contact with ALA 123 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54J VAL 3.6 0.2 - - - +
55J GLN* 3.4 2.9 - - - -
56J ILE* 2.8 39.8 + - + +
61J LEU* 4.5 11.4 - - + -
87J LYS* 4.3 18.8 - - + -
88J PHE* 3.6 27.1 - - - +
89J PRO* 3.7 4.5 - - + +
90J PHE 4.5 0.2 - - - +
122J ALA* 1.3 74.1 - - - +
124J ARG* 1.3 63.0 + - - +
125J VAL* 3.5 6.8 + - + +
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Residues in contact with ARG 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004A C 4.3 13.2 + - - -
1005A A 6.0 0.6 + - - -
9J SER* 3.5 29.1 + - - +
11J LYS* 2.7 36.8 + - - +
13J ALA* 4.0 20.6 - - - +
54J VAL 3.5 3.4 - - - +
55J GLN* 2.7 37.6 - - + +
87J LYS* 5.0 3.8 + - - +
88J PHE 5.1 0.2 + - - -
91J HIS* 3.1 28.7 + - + +
122J ALA 4.1 1.2 + - - -
123J ALA* 1.3 71.5 - - - +
125J VAL* 1.3 61.6 + - - +
126J HIS* 4.2 14.9 + - + +
129J ASN* 5.5 0.2 - - - +
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Residues in contact with VAL 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J VAL* 3.7 30.7 - - + -
52J LYS 3.8 0.9 - - - +
53J PRO* 3.0 2.8 - - - +
54J VAL* 2.8 41.3 + - + +
56J ILE* 4.2 17.5 - - + -
87J LYS* 4.1 26.5 - - + +
123J ALA* 4.0 12.3 - - + +
124J ARG* 1.3 77.4 - - - +
126J HIS* 1.3 74.7 + - - +
129J ASN* 4.0 17.3 - - + +
131J ILE* 4.8 8.1 - - + -
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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