Contacts of the strand formed by residues 117 - 126 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A LEU* 2.6 49.9 + - + +
115A GLY 3.3 0.5 + - - -
116A ALA* 1.3 83.6 - - + +
118A VAL* 1.3 68.4 + - - +
119A GLN* 2.8 35.0 + - + +
144A SER* 3.5 15.7 + - - -
145A PHE 3.5 11.4 - - - +
146A ASP* 4.0 15.6 - - + +
152A LYS* 4.5 11.4 + - - -
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Residues in contact with VAL 118 (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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3A ILE* 4.0 16.4 - - + -
17A LEU* 4.1 29.3 - - + +
111A VAL* 3.9 18.4 - - + -
112A THR 3.3 9.4 - - - +
113A ASP* 3.6 23.6 - - - +
115A GLY 4.7 5.2 - - - +
117A GLU* 1.3 82.1 - - - +
119A GLN* 1.3 72.1 + - - +
120A VAL* 5.0 0.4 - - + -
144A SER* 3.3 4.2 - - - -
145A PHE 3.1 30.2 + - - +
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Residues in contact with GLN 119 (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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110A GLU 4.0 0.3 - - - +
111A VAL* 3.4 5.0 - - - +
112A THR* 2.7 52.8 + - - +
114A LEU* 3.7 24.6 - - + +
117A GLU* 2.8 31.0 + - + +
118A VAL* 1.3 75.8 - - - +
120A VAL* 1.3 64.5 + - - +
121A LYS* 4.1 2.2 - - + +
142A THR* 3.9 19.4 - - + +
143A HIS 3.7 2.9 - - - -
144A SER* 3.7 6.7 - - - -
152A LYS* 5.5 3.4 - - - +
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Residues in contact with VAL 120 (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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15A ILE* 4.1 24.7 - - + -
17A LEU* 4.5 18.8 - - + -
27A PHE* 4.5 7.9 - - + -
109A TYR* 4.0 22.9 - - + -
110A GLU 3.6 3.6 - - - +
111A VAL* 4.4 8.5 - - + -
118A VAL* 5.0 0.2 - - + -
119A GLN* 1.3 78.3 - - - +
121A LYS* 1.3 59.6 + - - +
122A PHE* 3.4 37.1 - - + -
142A THR* 3.3 2.8 - - - -
143A HIS* 2.9 37.3 + - + +
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Residues in contact with LYS 121 (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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109A TYR* 3.0 4.5 - - - -
110A GLU* 2.9 46.3 + - + +
112A THR* 6.2 0.7 - - - +
119A GLN* 4.1 2.2 - - + -
120A VAL* 1.3 71.0 - - - +
122A PHE* 1.3 67.1 + - - +
123A SER* 4.1 10.1 + - - +
140A SER* 3.9 23.9 + - - -
141A VAL 3.8 2.7 - - - +
142A THR* 3.5 22.4 - - + +
156A GLU* 5.5 5.3 + - - -
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Residues in contact with PHE 122 (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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15A ILE* 4.1 4.9 - - + -
27A PHE* 4.0 20.9 - - + -
28A THR 3.7 5.2 - - - -
29A ASN* 3.4 38.8 - - + -
32A ALA* 3.7 14.4 - - + -
107A TRP* 3.6 19.1 - - + -
108A THR 3.2 7.4 - - - +
109A TYR* 3.6 19.1 - + + -
120A VAL* 3.4 32.8 - - + -
121A LYS* 1.3 72.6 - - - +
123A SER* 1.4 61.0 + - - +
140A SER* 3.1 5.4 - - - -
141A VAL 2.9 43.2 + - - +
143A HIS* 3.6 28.9 - + - -
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Residues in contact with SER 123 (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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107A TRP* 3.5 5.5 - - - +
108A THR* 2.8 44.4 + - - -
121A LYS* 4.6 11.8 + - - +
122A PHE* 1.4 75.4 + - - +
124A LEU* 1.3 65.5 + - - +
139A MET 3.3 9.6 - - - -
140A SER* 4.1 9.2 - - - -
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Residues in contact with LEU 124 (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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102A ILE* 4.0 13.5 - - + -
105A LYS* 4.0 23.3 - - + -
106A LEU 4.1 20.0 - - - +
107A TRP* 3.6 32.7 - - + +
108A THR 5.5 0.2 - - - +
123A SER* 1.3 79.6 - - - +
125A VAL* 1.3 73.3 + - - +
126A SER* 5.8 0.4 - - - -
138A GLU* 3.9 0.7 - - - -
139A MET* 2.8 59.5 + - + +
105B LYS* 5.6 10.3 - - + -
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Residues in contact with VAL 125 (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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124A LEU* 1.3 88.0 - - - +
126A SER* 1.3 74.9 + - - +
127A ASN* 3.7 3.3 + - - +
136A LYS* 4.1 16.4 - - + -
137A ILE 3.6 5.2 - - - +
138A GLU* 4.4 22.9 - - + +
100B GLU* 3.8 41.3 - - + +
105B LYS* 3.2 24.7 + - - +
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Residues in contact with SER 126 (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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67A PRO* 4.7 10.3 - - - +
102A ILE* 5.4 6.7 - - - +
124A LEU* 4.1 1.7 + - - -
125A VAL* 1.3 70.3 - - - +
127A ASN* 1.4 65.3 + - - +
130A THR* 3.8 22.6 + - - +
133A TYR* 5.3 3.1 - - - +
136A LYS* 3.1 2.9 - - - +
137A ILE* 2.8 60.4 + - - +
139A MET* 4.4 16.5 - - - +
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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