Contacts of the helix formed by residues 94 - 107 (chain c) in PDB entry 3J7Y
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 94 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92c PHE 3.4 3.2 + - - +
93c VAL* 1.3 75.3 - - - +
95c SER* 1.3 70.8 + - - +
96c CYS* 3.4 13.8 - - - +
97c TYR* 3.4 4.2 + - - +
98c ILE* 3.1 30.8 + - - +
121c SER* 3.9 3.1 - - - -
122c ASN* 3.1 24.8 + - - +
180c LEU 3.7 18.1 + - - +
181c SER* 4.3 9.6 - - - -
190c VAL* 3.4 33.8 + - - +
193c GLN* 4.6 14.0 + - - +
194c THR* 3.5 12.7 - - - +
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Residues in contact with SER 95 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94c ASN* 1.3 76.0 + - - +
96c CYS* 1.3 74.3 + - - +
98c ILE* 3.2 11.0 + - - +
99c LYS* 2.9 40.4 + - - +
121c SER* 3.6 15.8 + - - -
123c GLN* 4.7 13.0 + - - +
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Residues in contact with CYS 96 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94c ASN* 3.4 14.8 - - + +
95c SER* 1.3 84.5 + - - +
97c TYR* 1.3 58.1 + - - +
99c LYS* 3.2 13.0 + - - +
100c SER* 2.9 28.8 + - - -
181c SER* 5.6 1.3 - - - -
182c GLU* 3.6 37.2 - - + +
190c VAL* 4.9 13.2 - - - -
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Residues in contact with TYR 97 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93c VAL* 4.1 17.5 - - + -
94c ASN* 3.4 8.5 + - - +
95c SER 3.2 0.4 - - - -
96c CYS* 1.3 78.1 - - - +
98c ILE* 1.3 60.5 + - - +
100c SER* 2.5 30.0 + - - -
101c GLU* 2.9 35.2 + - + +
104c LYS* 6.2 1.8 - - - -
119c LEU* 4.6 12.8 - - + -
180c LEU* 3.2 58.7 - - + +
181c SER* 3.7 11.2 - - - -
182c GLU 3.8 7.6 - - - +
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Residues in contact with ILE 98 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93c VAL* 3.6 25.1 - - + -
94c ASN 3.1 17.8 + - - +
95c SER* 3.2 9.6 + - - +
97c TYR* 1.3 82.5 - - + +
99c LYS* 1.3 58.1 + - + +
101c GLU* 3.2 12.2 + - - +
102c GLU* 2.9 48.4 + - + +
119c LEU* 4.4 26.2 - - + +
121c SER* 3.9 25.1 - - - +
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Residues in contact with LYS 99 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95c SER* 2.9 21.9 + - - +
96c CYS* 3.2 14.8 + - - +
98c ILE* 1.3 78.6 - - + +
100c SER* 1.3 57.6 + - - +
102c GLU* 3.2 14.2 + - - +
103c ALA* 2.9 29.9 + - - +
182c GLU* 5.8 0.9 - - - +
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Residues in contact with SER 100 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96c CYS 2.9 12.3 + - - -
97c TYR* 2.5 32.1 + - - -
99c LYS* 1.3 77.1 - - - +
101c GLU* 1.3 55.6 + - - +
103c ALA* 3.2 9.7 + - - +
104c LYS* 2.9 46.8 + - - +
182c GLU* 4.5 19.8 - - - +
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Residues in contact with GLU 101 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97c TYR* 2.9 29.6 + - + +
98c ILE* 3.3 16.2 - - - +
100c SER* 1.3 80.9 + - - +
102c GLU* 1.3 60.0 + - - +
104c LYS* 3.2 14.3 + - + +
105c ARG* 2.9 66.0 + - + +
119c LEU* 4.0 23.9 - - - +
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Residues in contact with GLU 102 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98c ILE* 2.9 32.7 + - + +
99c LYS* 3.4 15.4 - - - +
101c GLU* 1.3 80.5 - - + +
103c ALA* 1.3 57.0 + - - +
105c ARG* 3.2 19.1 + - - +
106c GLN* 2.9 36.5 + - + +
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Residues in contact with ALA 103 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99c LYS 2.9 13.0 + - - +
100c SER* 3.2 13.2 + - - +
102c GLU* 1.3 77.1 - - - +
104c LYS* 1.3 56.8 - - + +
106c GLN* 3.2 13.6 + - - +
107c GLN* 2.9 42.7 + - - +
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Residues in contact with LYS 104 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97c TYR* 6.2 1.8 - - - -
100c SER* 2.9 30.8 + - - +
101c GLU* 3.4 13.0 - - + +
103c ALA* 1.3 76.4 - - + +
105c ARG* 1.3 64.2 + - + +
107c GLN* 3.2 31.4 + - - +
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Residues in contact with ARG 105 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101c GLU* 2.9 49.7 + - + +
102c GLU* 3.4 18.4 - - - +
104c LYS* 1.3 78.9 - - + +
106c GLN* 1.3 62.7 + - + +
107c GLN 4.0 4.0 - - - -
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Residues in contact with GLN 106 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102c GLU* 2.9 17.5 + - + +
103c ALA* 3.2 15.1 + - - +
105c ARG* 1.3 79.1 - - + +
107c GLN* 1.3 63.1 + - + +
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Residues in contact with GLN 107 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103c ALA* 2.9 27.6 + - - +
104c LYS* 3.2 26.7 + - - +
105c ARG 4.0 3.6 - - - -
106c GLN* 1.3 83.0 - - + +
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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