Contacts of the helix formed by residues 97 - 106 (chain B) in PDB entry 1N1J
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 GLN 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ALA* 4.7 7.9 - - + -
80A ALA* 4.0 6.1 - - - -
93B ARG* 3.4 38.2 - - - +
95B THR* 3.5 19.1 - - + +
96B LEU* 1.3 81.9 - - - +
98B ARG* 1.3 65.6 + - - +
99B ASN* 2.8 27.2 + - - +
100B ASP* 2.9 26.0 + - - +
101B ILE* 3.3 3.6 + - - +
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Residues in contact with ARG 98 (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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77A ALA* 5.6 0.2 - - - +
79A ASP* 2.9 55.7 + - - +
80A ALA* 4.0 5.8 - - - +
82A GLU* 4.3 3.0 + - - +
83A CYS* 3.6 28.7 - - + +
86A GLU* 3.2 38.4 + - - -
97B GLN* 1.3 73.0 - - - +
99B ASN* 1.3 58.7 + - - +
101B ILE* 3.0 15.4 + - - +
102B ALA* 2.9 25.3 + - + +
117B ILE 5.0 3.2 + - - -
118B VAL* 4.0 14.0 - - + +
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Residues in contact with ASN 99 (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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91B ASN* 5.4 2.2 - - - +
93B ARG* 3.9 15.6 - - - +
97B GLN* 2.8 36.5 + - - +
98B ARG* 1.3 78.3 - - - +
100B ASP* 1.3 62.9 + - - +
102B ALA* 3.7 8.9 - - - +
103B MET* 3.0 26.9 + - - +
120B ARG* 5.4 1.8 + - - +
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Residues in contact with ASP 100 (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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84B ALA* 3.4 25.0 - - + +
87B HIS* 3.7 13.7 - - - +
88B THR* 2.8 32.5 + - - +
91B ASN* 4.2 1.4 + - - -
93B ARG* 2.8 40.8 + - - -
96B LEU* 4.6 0.2 - - + -
97B GLN 2.9 21.3 + - - +
99B ASN* 1.3 78.6 + - - +
101B ILE* 1.3 60.8 + - - +
103B MET* 3.4 3.2 + - - +
104B ALA* 3.0 27.5 + - - +
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Residues in contact with ILE 101 (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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80A ALA* 3.6 29.4 - - + +
83A CYS* 3.7 29.6 - - + -
84A VAL* 3.8 14.8 - - + -
87A CYS* 4.5 1.3 - - - -
80B LEU* 4.1 23.6 - - + -
81B THR* 6.3 0.4 - - - -
84B ALA* 3.7 20.6 - - + -
96B LEU* 3.9 14.8 - - + -
97B GLN 3.8 7.0 - - - +
98B ARG* 3.0 7.1 + - - +
100B ASP* 1.3 74.9 - - - +
102B ALA* 1.3 66.0 + - - +
104B ALA* 3.1 3.9 + - - +
105B ILE* 3.0 38.5 + - + +
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Residues in contact with ALA 102 (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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98B ARG* 2.9 12.9 + - + +
99B ASN* 3.7 12.6 - - - +
100B ASP 3.4 0.2 - - - -
101B ILE* 1.3 79.2 - - - +
103B MET* 1.3 63.4 + - - +
105B ILE* 3.4 8.4 + - - +
106B THR* 3.4 18.7 + - - +
118B VAL* 3.3 32.7 - - + +
119B PRO 3.5 21.1 - - - +
120B ARG* 3.7 9.9 - - - +
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Residues in contact with MET 103 (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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87B HIS* 3.3 37.5 - - + +
99B ASN 3.0 17.7 + - - +
100B ASP 3.6 5.6 - - - +
102B ALA* 1.3 76.6 - - - +
104B ALA* 1.3 62.7 + - - +
106B THR* 2.8 27.9 + - - -
107B LYS* 3.5 24.5 - - - +
120B ARG* 3.5 47.9 - - - +
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Residues in contact with ALA 104 (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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80B LEU* 4.7 7.2 - - + +
83B ARG* 3.6 39.3 + - + +
84B ALA* 3.7 4.7 - - + +
87B HIS* 3.6 10.7 - - - -
100B ASP 3.0 17.2 + - - +
101B ILE* 3.5 6.5 - - - +
103B MET* 1.3 75.1 - - - +
105B ILE* 1.3 62.9 + - - +
107B LYS* 3.0 15.6 + - - +
108B PHE* 3.6 9.2 + - - +
111B PHE* 4.1 6.8 - - + -
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Residues in contact with ILE 105 (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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87A CYS* 4.5 0.7 - - - -
80B LEU* 4.4 8.3 - - + -
101B ILE* 3.0 28.4 + - + +
102B ALA* 3.6 8.3 - - - +
103B MET 3.2 0.2 - - - -
104B ALA* 1.3 78.6 - - - +
106B THR* 1.3 61.4 + - + +
107B LYS 3.2 1.4 + - - -
108B PHE 3.5 16.1 - - - +
111B PHE* 3.4 31.0 - - + +
112B ASP* 4.7 2.1 + - - +
114B LEU* 3.7 29.8 - - + +
115B ILE* 3.7 30.8 - - + +
118B VAL* 3.6 35.7 - - + +
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Residues in contact with THR 106 (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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102B ALA 3.4 15.5 - - - +
103B MET* 2.8 21.9 + - - -
105B ILE* 1.3 80.3 - - + +
107B LYS* 1.3 73.9 + - - +
108B PHE 3.6 0.7 - - - -
112B ASP* 6.2 0.2 - - - -
115B ILE* 5.2 17.5 - - + -
118B VAL 6.0 0.2 - - - +
120B ARG* 3.8 22.8 + - + +
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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