Contacts of the strand formed by residues 117 - 126 (chain B) in PDB entry 1NSX
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 GLU 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B LEU* 2.7 41.6 + - + +
115B GLY 3.1 1.3 + - - -
116B ALA* 1.3 81.7 - - + +
118B VAL* 1.3 68.5 + - - +
119B GLN* 3.0 30.9 + - + +
144B SER* 3.8 20.5 + - - -
145B PHE 3.6 11.9 - - - +
146B ASP* 4.2 14.8 - - + +
152B LYS* 4.8 11.4 + - - -
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Residues in contact with VAL 118 (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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2B SER 5.9 2.2 - - - +
3B ILE* 4.1 16.6 - - + -
17B LEU* 3.8 39.6 - - + +
111B VAL* 4.1 18.6 - - + -
112B THR 3.6 8.1 - - - +
113B ASP* 3.8 17.3 - - - +
115B GLY 4.8 5.2 - - - +
117B GLU* 1.3 80.2 - - - +
119B GLN* 1.3 66.8 + - - +
120B VAL* 4.7 0.4 - - + -
143B HIS 4.1 0.5 - - - +
144B SER* 3.2 3.5 - - - -
145B PHE 3.1 31.0 + - - +
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Residues in contact with GLN 119 (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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110B GLU 3.9 0.9 - - - +
111B VAL* 3.4 5.2 - - - +
112B THR* 2.8 52.3 + - - +
114B LEU* 3.4 25.5 - - + +
117B GLU* 3.0 26.8 + - - +
118B VAL* 1.3 77.5 - - - +
120B VAL* 1.3 64.1 + - - +
121B LYS* 3.9 1.8 - - + +
142B THR* 3.8 19.7 - - + +
143B HIS 3.6 3.8 - - - -
144B SER* 3.9 5.6 - - - -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 4.1 26.0 - - + -
17B LEU* 4.5 16.8 - - + -
27B PHE* 4.7 7.2 - - + -
109B TYR* 4.1 21.1 - - + -
110B GLU 3.8 2.9 - - - +
111B VAL* 4.4 8.3 - - + -
118B VAL* 4.7 3.6 - - + -
119B GLN* 1.3 77.0 - - - +
121B LYS* 1.3 59.4 + - - +
122B PHE* 3.5 37.8 - - + -
141B VAL 3.5 2.8 - - - +
142B THR* 3.3 2.0 - - - -
143B HIS* 2.8 43.9 + - + +
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Residues in contact with LYS 121 (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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108B THR 4.0 0.2 - - - +
109B TYR* 3.1 4.5 - - - -
110B GLU* 3.0 39.1 + - + +
119B GLN* 3.9 2.1 - - + -
120B VAL* 1.3 72.2 - - - +
122B PHE* 1.3 62.5 + - - +
123B SER* 4.2 9.8 + - - +
140B SER* 3.6 32.8 - - - -
141B VAL 3.7 3.1 - - - +
142B THR* 3.5 23.3 - - + +
156B GLU* 4.7 8.6 + - - -
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Residues in contact with PHE 122 (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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15B ILE* 4.2 4.5 - - + -
27B PHE* 4.1 14.8 - - + -
28B THR 3.8 9.4 - - - -
29B ASN* 3.4 39.9 - - + -
32B ALA* 3.8 15.3 - - + -
107B TRP* 3.6 19.8 - - + -
108B THR 3.3 7.4 - - - +
109B TYR* 3.5 20.6 - + + -
120B VAL* 3.5 31.0 - - + -
121B LYS* 1.3 70.5 - - - +
123B SER* 1.3 63.4 + - - +
140B SER* 3.1 6.1 - - - -
141B VAL 2.8 47.1 + - - +
143B HIS* 3.5 28.3 - + - -
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Residues in contact with SER 123 (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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107B TRP* 3.4 5.9 - - - +
108B THR* 2.8 45.7 + - - +
109B TYR* 5.9 0.4 - - - -
121B LYS* 4.2 12.3 + - - +
122B PHE* 1.3 78.4 + - - +
124B LEU* 1.3 67.0 + - - +
139B MET 3.4 8.5 - - - -
140B SER* 3.8 10.6 - - - -
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Residues in contact with LEU 124 (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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105A LYS* 5.4 11.0 - - + -
102B ILE* 4.1 11.2 - - + -
105B LYS* 4.0 22.0 - - + -
106B LEU 4.1 19.7 - - - +
107B TRP* 3.6 38.1 - - + +
123B SER* 1.3 78.4 - - - +
125B VAL* 1.3 76.8 + - - +
126B SER* 5.9 0.2 - - - -
139B MET* 2.8 51.5 + - + +
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Residues in contact with VAL 125 (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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100A GLU* 3.9 33.2 - - + +
105A LYS* 3.1 26.6 + - - +
124B LEU* 1.3 89.3 - - - +
126B SER* 1.3 72.1 + - - +
127B ASN* 3.6 2.8 + - - +
136B LYS* 4.0 24.0 - - + -
137B ILE 3.4 7.2 - - - +
138B GLU* 4.4 20.4 - - + -
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Residues in contact with SER 126 (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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67B PRO* 4.8 10.3 - - - +
102B ILE* 5.4 3.8 - - - +
124B LEU* 5.9 0.4 - - - -
125B VAL* 1.3 72.5 - - - +
127B ASN* 1.3 63.1 + - - +
130B THR* 3.8 21.6 + - - +
133B TYR* 5.1 3.8 - - - +
136B LYS* 3.2 1.4 - - - +
137B ILE* 2.8 60.5 + - - +
139B MET* 3.9 19.8 - - - +
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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