Contacts of the helix formed by residues 141 - 150 (chain J) in PDB entry 1NJI
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 ASN 141 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71J TYR* 3.5 12.9 + - + -
72J VAL* 5.7 5.6 - - + -
74J ASN* 2.7 42.8 + - + +
75J SER* 4.3 10.5 + - - +
139J ASP* 2.8 41.9 + - - +
140J PRO* 1.3 71.0 - - - +
142J VAL* 1.3 60.8 + - - +
143J GLU 3.2 1.1 - - - -
144J GLU* 3.0 24.1 + - - +
145J ALA* 3.0 10.5 + - - +
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Residues in contact with VAL 142 (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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46J VAL* 4.2 9.9 - - + -
72J VAL* 5.1 11.8 - - + +
83J PHE* 5.1 1.8 - - + -
134J ALA* 3.5 30.7 - - + -
136J VAL* 3.6 28.7 - - + -
140J PRO* 3.5 21.3 - - + -
141J ASN* 1.3 76.8 - - - +
143J GLU* 1.3 66.2 + - - +
144J GLU 2.9 1.8 - - - -
145J ALA* 2.9 20.8 + - + +
146J TRP* 3.1 35.4 + - + +
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Residues in contact with GLU 143 (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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46J VAL* 4.7 14.1 - - + +
140J PRO* 4.0 29.4 - - + +
141J ASN 3.2 0.2 - - - -
142J VAL* 1.3 82.8 - - - +
144J GLU* 1.3 60.7 + - - +
146J TRP* 4.9 0.4 - - - -
147J ARG* 3.4 6.9 + - - +
159J ILE* 3.4 52.5 - - + +
161J SER* 5.0 7.3 - - - -
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Residues in contact with GLU 144 (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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71J TYR* 3.6 29.2 - - + +
140J PRO 5.4 0.7 - - - +
141J ASN* 3.0 16.9 + - - +
142J VAL 2.9 0.6 - - - -
143J GLU* 1.3 77.9 - - - +
145J ALA* 1.3 62.9 + - - +
146J TRP 3.0 2.9 + - - -
147J ARG* 3.1 52.0 + - - +
148J ARG* 3.3 19.8 + - - +
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Residues in contact with ALA 145 (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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68J ALA* 3.2 49.0 - - + +
71J TYR* 3.7 18.6 - - + -
72J VAL* 4.8 7.9 - - + +
83J PHE* 5.3 2.7 - - + -
141J ASN 3.0 4.8 + - - +
142J VAL* 2.9 19.5 + - + +
144J GLU* 1.3 77.6 - - - +
146J TRP* 1.3 61.4 + - + +
148J ARG* 3.7 4.1 + - - +
149J ALA 3.2 11.8 + - - -
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Residues in contact with TRP 146 (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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46J VAL* 2.6 62.1 - - + -
47J GLU* 3.0 22.2 - - - -
48J LEU* 3.8 16.8 - - + +
83J PHE* 2.9 46.2 - + - -
132J PHE* 3.8 18.9 - - + +
133J ILE* 3.9 0.2 - - - -
134J ALA* 3.3 19.1 - - + -
142J VAL* 3.1 15.1 + - + +
144J GLU 3.0 0.6 - - - -
145J ALA* 1.3 83.1 - - + +
147J ARG* 1.3 66.3 + - - +
148J ARG 2.9 2.2 - - - -
149J ALA* 2.9 22.1 + - + +
150J LYS* 3.0 20.6 + - - +
159J ILE* 3.7 22.2 - - + -
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Residues in contact with ARG 147 (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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1135A G 4.2 16.8 - - - +
2502A C 3.0 18.6 + - - -
2503A A 2.4 31.7 + - - -
143J GLU 3.4 8.5 + - - +
144J GLU* 3.1 44.1 + - - +
146J TRP* 1.3 77.3 - - - +
148J ARG* 1.3 78.1 + - - +
150J LYS* 3.3 33.0 + - - +
151J MET* 3.6 22.2 - - - +
159J ILE* 4.0 1.3 - - + +
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Residues in contact with ARG 148 (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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2502A C 4.3 9.0 + - - +
2503A A 4.1 26.5 + - - -
2504A A 2.9 36.1 + - - -
67J ALA* 4.1 27.3 + - + +
70J ARG* 5.9 0.6 - - - +
71J TYR* 3.8 39.8 - - - +
144J GLU* 3.3 18.3 + - - +
145J ALA 3.7 8.3 - - - +
146J TRP 2.9 0.4 - - - -
147J ARG* 1.3 100.4 - - - +
149J ALA* 1.3 59.5 + - - +
151J MET* 2.9 22.9 - - - +
152J LYS* 3.9 9.0 + - - +
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Residues in contact with ALA 149 (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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48J LEU* 4.0 10.3 - - + -
64J ALA* 3.8 36.9 - - - +
68J ALA* 4.0 7.0 - - + -
132J PHE* 4.4 9.6 - - + -
145J ALA 3.2 14.9 + - - +
146J TRP* 2.9 20.2 + - + +
148J ARG* 1.3 72.4 - - - +
150J LYS* 1.3 56.4 + - - +
151J MET 2.8 10.1 + - - -
152J LYS* 3.0 15.4 + - - -
153J VAL* 3.8 4.1 + - - +
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Residues in contact with LYS 150 (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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1134A G 3.8 16.5 + - - +
1135A G 4.6 16.9 + - - -
48J LEU* 4.1 9.1 - - + +
146J TRP 3.0 24.3 + - - +
147J ARG* 3.3 37.2 - - - +
149J ALA* 1.3 74.6 - - - +
151J MET* 1.3 60.4 + - - +
152J LYS 3.3 0.4 - - - -
153J VAL* 3.6 15.0 - - - +
157J ILE* 3.4 48.2 - - + -
159J ILE* 3.9 16.4 - - + +
8309J NA 2.9 26.3 - - - -
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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