Contacts of the strand formed by residues 109 - 117 (chain B) in PDB entry 1NRJ
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 VAL 109 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B SER* 3.5 22.7 - - - +
42B ILE* 3.9 27.6 - - + -
101B TYR* 4.2 7.9 - - + -
102B LEU* 4.5 2.7 - - + -
105B ARG* 3.7 14.4 - - + +
106B ALA* 3.1 18.8 + - - +
107B LYS 3.5 1.3 - - - +
108B PHE* 1.3 78.6 - - - +
110B LYS* 1.3 60.7 + - - +
111B GLY 3.6 22.4 - - - +
112B LEU* 5.4 0.7 - - + -
147B ILE* 3.9 28.8 - - + +
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Residues in contact with LYS 110 (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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39B PRO* 3.8 29.6 - - + +
40B SER 2.8 19.1 + - - +
41B ILE* 4.3 6.3 - - + -
83B VAL* 4.2 13.6 - - + +
108B PHE 4.1 1.8 - - - +
109B VAL* 1.3 74.2 - - - +
111B GLY* 1.3 53.7 + - - +
147B ILE* 4.6 1.7 - - - +
148B ASP* 4.8 6.6 + - - +
243B LYS* 3.0 40.2 + - - +
244B LEU 2.7 32.3 + - - -
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Residues in contact with GLY 111 (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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40B SER 4.0 1.0 + - - -
41B ILE* 3.5 9.5 - - - +
42B ILE 3.2 20.1 + - - -
109B VAL* 3.4 8.5 - - - +
110B LYS* 1.3 79.4 - - - +
112B LEU* 1.4 59.8 + - - -
113B ILE 4.3 0.2 - - - -
147B ILE* 3.7 8.5 - - - +
148B ASP 3.5 12.6 - - - -
239B TRP* 3.9 17.3 - - - -
243B LYS* 4.7 1.3 - - - -
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Residues in contact with LEU 112 (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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42B ILE* 3.5 41.5 - - + +
44B ALA* 4.5 10.8 - - + -
98B LEU* 4.7 6.1 - - + -
102B LEU* 4.9 5.2 - - + -
109B VAL* 5.4 0.4 - - + -
111B GLY* 1.4 75.5 - - - +
113B ILE* 1.3 78.1 + - - +
114B PHE* 3.8 14.4 - - + +
132B LEU* 5.8 0.4 - - + -
135B ILE* 3.9 30.1 - - + -
139B THR* 5.0 4.5 - - + -
147B ILE* 3.9 6.2 - - + +
148B ASP 3.0 7.3 + - - +
149B ILE* 3.2 26.8 - - + +
150B LEU 3.0 23.6 + - - -
239B TRP* 3.7 1.6 - - - -
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Residues in contact with ILE 113 (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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41B ILE* 4.4 7.2 - - + -
42B ILE 2.8 15.9 + - - +
43B ILE* 3.5 22.1 - - + +
44B ALA 2.9 28.6 + - - +
54B LEU* 4.5 10.5 - - + -
112B LEU* 1.3 75.2 - - - +
114B PHE* 1.3 58.5 + - - +
115B MET* 3.9 12.6 - - + -
150B LEU* 3.4 17.3 - - + +
152B ALA* 3.8 27.6 - - + -
236B TRP* 6.0 1.1 - - + -
239B TRP* 3.6 20.0 - - + -
240B ILE* 4.1 34.3 - - + -
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Residues in contact with PHE 114 (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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44B ALA 3.4 2.5 - - - -
45B GLY* 3.8 19.3 - - - -
46B PRO* 4.0 8.7 - - + -
112B LEU* 3.8 10.9 - - + +
113B ILE* 1.3 70.5 - - - +
115B MET* 1.3 60.1 + - - +
116B VAL* 3.8 15.4 + - + -
128B THR* 3.7 42.8 - - + -
131B PHE* 4.1 11.4 - + + -
132B LEU* 3.9 38.1 - - + -
135B ILE* 3.8 30.1 - - + -
149B ILE* 4.4 6.1 - - + -
150B LEU 2.8 12.0 + - - +
151B ILE* 3.4 15.6 - - + +
152B ALA 3.0 20.9 + - - -
171B LEU* 5.0 1.6 - - + -
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Residues in contact with MET 115 (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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43B ILE* 4.0 7.2 - - + -
44B ALA 2.9 12.4 + - - +
45B GLY* 3.7 0.9 - - - -
46B PRO* 3.2 25.6 - - - +
49B SER* 3.4 18.7 + - - +
50B GLY 3.6 27.8 - - - +
51B LYS* 3.6 16.4 - - + -
54B LEU* 3.9 15.9 - - + -
113B ILE* 3.9 20.0 - - + -
114B PHE* 1.3 72.7 - - - +
116B VAL* 1.3 61.4 + - - +
152B ALA* 3.5 8.7 - - + -
154B ASN* 3.7 28.3 - - + +
228B ILE* 3.7 19.5 - - + -
236B TRP* 3.8 16.4 - - + -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 4.4 5.8 - - + -
49B SER* 3.8 8.3 - - - -
114B PHE* 3.8 26.9 - - + +
115B MET* 1.3 80.3 - - - +
117B ASP* 1.3 66.9 + - - +
125B LEU* 6.4 1.3 - - + -
128B THR* 4.1 15.0 - - + -
151B ILE* 4.5 6.7 - - + -
152B ALA 3.1 13.3 + - - +
153B CYS* 4.0 23.1 - - + -
154B ASN* 2.9 30.7 + - - +
167B ILE* 4.2 17.3 - - + -
171B LEU* 5.0 4.7 - - + -
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Residues in contact with ASP 117 (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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46B PRO* 6.0 0.4 - - - +
48B ASN* 4.1 16.6 + - + +
49B SER* 3.9 8.0 - - - -
116B VAL* 1.3 75.5 - - - +
118B SER* 1.4 61.1 + - - +
119B THR* 2.8 33.6 + - - +
120B VAL* 3.2 32.0 + - + +
154B ASN 4.3 2.7 - - - -
155B LYS* 3.0 46.1 + - - +
158B LEU* 5.9 0.2 - - - +
167B ILE* 5.4 0.3 - - - +
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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