Contacts of the strand formed by residues 137 - 146 (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 ILE 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A PRO* 4.5 15.5 - - + -
124A LEU 3.8 0.2 - - - +
125A VAL* 3.6 1.8 - - - -
126A SER* 2.8 45.7 + - - +
133A TYR* 5.1 4.0 - - + -
134A PRO 4.0 20.4 - - - +
135A GLY* 4.1 1.1 - - - -
136A LYS* 1.3 78.4 - - - +
138A GLU* 1.3 62.8 + - - +
139A MET* 3.5 21.8 + - + +
157A ALA* 3.9 16.2 - - + -
158A ILE 3.3 11.4 - - - +
159A SER* 4.0 10.8 - - - +
163A THR* 4.2 12.8 - - + +
164A VAL 4.6 1.3 - - - +
165A PHE* 4.1 24.7 - - + -
322A LEU* 5.0 2.0 - - + -
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Residues in contact with GLU 138 (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 3.9 3.6 - - - -
125A VAL* 4.4 14.9 - - + +
136A LYS* 3.0 36.0 - - + +
137A ILE* 1.3 73.7 - - - +
139A MET* 1.3 58.3 + - - +
156A GLU 4.1 0.3 - - - +
157A ALA* 3.3 4.9 - - - -
158A ILE* 2.7 43.9 + - + +
160A ASP* 5.7 1.8 - - - +
100B GLU* 5.7 1.0 - - - +
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Residues in contact with MET 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO* 5.4 2.9 - - - -
102A ILE* 4.1 25.8 - - + -
107A TRP* 4.1 15.5 - - + -
123A SER* 3.3 5.5 - - - -
124A LEU* 2.8 74.9 + - + +
126A SER* 4.4 17.7 - - - +
137A ILE* 3.9 12.1 - - + +
138A GLU* 1.3 76.2 - - - +
140A SER* 1.3 62.7 + - - +
141A VAL* 5.7 0.7 - - + -
156A GLU 3.6 7.0 - - - +
165A PHE* 3.8 36.3 - - + -
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Residues in contact with SER 140 (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* 4.4 0.9 - - - -
121A LYS* 3.9 28.7 + - - +
122A PHE 3.1 12.3 - - - -
123A SER* 4.1 5.6 - - - -
139A MET* 1.3 75.4 - - - +
141A VAL* 1.3 66.6 + - - +
142A THR* 4.2 2.5 + - - -
154A HIS 5.2 0.3 + - - -
155A TYR* 3.5 3.6 - - - +
156A GLU* 3.0 48.6 + - - +
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Residues in contact with VAL 141 (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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32A ALA* 4.4 5.8 - - + -
64A THR* 3.9 28.3 - - + +
107A TRP* 3.7 28.3 - - + -
122A PHE* 2.9 34.2 + - - -
139A MET* 5.7 0.9 - - + -
140A SER* 1.3 82.0 - - - +
142A THR* 1.3 63.6 + - - +
143A HIS* 4.1 12.1 - - + +
153A ILE* 3.5 29.4 - - + -
154A HIS 3.5 4.3 - - - +
155A TYR* 4.1 14.1 - - + -
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Residues in contact with THR 142 (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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119A GLN* 3.9 33.7 - - + +
120A VAL 3.3 11.2 - - - +
121A LYS* 3.5 27.6 - - + +
140A SER* 4.9 1.9 + - - -
141A VAL* 1.3 75.3 + - - +
143A HIS* 1.3 64.3 + - - +
144A SER* 4.9 2.5 - - - -
152A LYS* 3.4 2.1 - - - +
153A ILE* 3.3 4.3 - - - -
154A HIS* 2.9 47.6 + - + +
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Residues in contact with HIS 143 (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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27A PHE* 3.7 36.7 - + + -
32A ALA 2.9 27.3 + - - -
33A ARG* 4.3 0.6 + - - -
34A ILE 4.9 4.0 - - - -
62A GLY 5.4 2.0 - - - -
64A THR* 4.9 1.8 - - - -
118A VAL 4.1 0.2 - - - +
119A GLN* 3.7 0.3 - - - -
120A VAL* 2.9 35.0 + - + +
122A PHE* 3.6 28.3 - + + -
141A VAL* 4.1 9.7 - - + +
142A THR* 1.3 73.7 - - - +
144A SER* 1.3 61.1 + - - +
151A TRP* 3.2 25.0 + + - +
152A LYS 3.3 3.6 - - - -
153A ILE* 3.9 31.7 - - + +
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Residues in contact with SER 144 (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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17A LEU* 5.1 1.3 - - - -
27A PHE* 5.3 1.3 - - - -
117A GLU* 3.5 26.7 + - - -
118A VAL 3.3 12.8 - - - -
119A GLN* 3.7 9.6 - - - -
142A THR* 4.9 4.2 - - - +
143A HIS* 1.3 76.2 - - - +
145A PHE* 1.3 61.5 + - - +
150A LYS 3.7 1.2 + - - +
151A TRP* 3.3 9.9 - - - -
152A LYS* 2.8 56.1 + - - +
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Residues in contact with PHE 145 (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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17A LEU* 3.9 19.4 - - + +
19A ASN* 3.6 30.2 - - + +
23A VAL* 3.6 33.2 - - + -
25A ILE* 3.3 34.5 - - + -
27A PHE* 5.3 0.4 - - + -
37A TRP* 3.7 29.2 - + - -
117A GLU* 3.5 2.5 - - - -
118A VAL* 3.1 29.4 + - - +
144A SER* 1.3 75.9 - - - +
146A ASP* 1.3 63.2 + - - +
149A ASN* 3.7 26.5 - - - -
150A LYS 3.5 15.7 - - - -
151A TRP* 4.1 8.1 - - + -
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Residues in contact with ASP 146 (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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19A ASN* 2.8 24.8 + - - +
116A ALA* 3.1 13.7 - - + +
117A GLU* 4.0 18.7 - - + +
145A PHE* 1.3 78.2 - - - +
147A ASP* 1.3 65.4 + - - +
148A ASP* 2.7 33.1 + - - +
149A ASN* 3.0 8.1 + - - -
150A LYS* 2.9 45.9 + - - +
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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