Contacts of the helix formed by residues 101 - 105 (chain v) in PDB entry 4IL6
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 PHE 101 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390c ARG* 3.4 33.7 - - + -
89v ALA 3.5 10.8 - - - -
91v VAL 3.6 22.2 - - - -
92v HIS 3.5 15.3 - - - -
93v PRO* 3.6 37.5 - - + -
97v SER* 2.8 28.3 + - - +
98v ALA* 3.1 8.5 - - - +
100v ILE* 1.3 81.5 - - + +
102v PRO* 1.3 58.7 - - - +
103v LYS* 3.1 5.8 - - + +
104v MET* 2.9 30.6 + - + +
201v HEM 5.2 7.6 - - + -
202v DMS 3.6 28.3 - - + -
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Residues in contact with PRO 102 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78c GLU* 3.3 34.8 - - - +
80c PRO* 6.4 1.6 - - + -
104c GLU* 5.0 0.4 - - - +
526c DMS 5.2 6.1 - - + -
528c DMS 3.4 25.6 - - - +
98v ALA 3.3 10.3 - - - +
99v ASP 4.1 1.3 - - - +
100v ILE 3.4 7.6 - - - +
101v PHE* 1.3 85.9 - - - +
103v LYS* 1.3 60.5 + - + +
104v MET 3.1 2.0 - - - -
105v ARG* 3.2 42.7 + - - +
202v DMS 3.8 17.5 - - + -
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Residues in contact with LYS 103 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78c GLU* 4.4 12.5 - - - +
79c LYS* 4.0 13.5 - - + -
80c PRO* 4.5 7.4 - - + -
83c GLU* 3.1 39.0 + - - +
398c HIS* 5.6 0.4 - - - -
34v GLN 5.3 1.0 + - - -
35v TYR* 2.8 69.5 + - + +
36v ALA* 4.1 17.5 - - + +
39v SER* 5.0 9.9 + - - -
101v PHE* 3.0 2.5 + - + -
102v PRO* 1.3 79.9 - - + +
104v MET* 1.3 64.2 + - + +
105v ARG 3.3 0.4 - - - -
106v ASN 4.8 0.3 + - - -
107v LEU* 3.9 11.3 - - - +
201v HEM 6.4 0.7 - - - -
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Residues in contact with MET 104 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36v ALA* 4.4 5.8 - - - -
76v MET* 4.0 13.5 - - + +
93v PRO* 3.9 11.7 - - + +
94v SER* 3.7 48.2 - - - +
95v LEU* 3.8 16.7 - - + +
98v ALA* 4.0 5.7 - - + +
101v PHE* 2.9 16.1 + - + +
103v LYS* 1.3 80.9 - - + +
105v ARG* 1.3 63.3 + - - +
106v ASN 3.4 2.0 - - - -
107v LEU* 3.3 42.2 + - + +
112v LEU* 4.5 6.5 - - + -
201v HEM 3.4 34.5 - - + -
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Residues in contact with ARG 105 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78c GLU* 4.7 14.4 - - + +
104c GLU* 2.7 33.9 + - - -
528c DMS 3.6 8.9 + - - +
98v ALA* 3.2 32.2 + - + +
99v ASP* 2.8 30.1 + - - +
102v PRO* 3.2 28.6 + - - +
103v LYS 3.3 0.2 - - - -
104v MET* 1.3 79.7 - - - +
106v ASN* 1.3 69.7 + - - +
107v LEU 3.7 1.4 + - - +
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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