Contacts of the helix formed by residues 113 - 118 (chain J) in PDB entry 6C6S
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 HIS 113 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1333I LEU* 4.4 4.3 - - + +
1334I GLY* 3.4 28.9 + - - -
1335I ILE* 5.4 1.6 - - + -
111J THR 3.4 3.0 + - - -
112J ALA* 1.3 72.1 - - - +
114J ILE* 1.3 65.1 + - - +
115J TRP* 3.2 54.5 + + + +
116J PHE* 3.3 27.8 + + + +
117J LEU* 3.2 18.5 + - - +
124J ILE* 4.5 2.3 - - - +
237J MET 3.3 24.6 + - - +
239J LEU* 3.5 33.7 - - + -
307J LEU* 3.5 24.3 - - + +
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Residues in contact with ILE 114 (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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112J ALA 3.4 3.0 + - - -
113J HIS* 1.3 71.8 + - - +
115J TRP* 1.3 63.3 + - + +
117J LEU* 3.6 11.4 - - + -
118J LYS* 2.9 54.3 + - + +
140J TYR* 4.3 2.5 - - - +
304J ASP* 3.4 52.3 + - + +
307J LEU* 4.1 11.4 - - + +
308J ASP* 4.2 20.6 - - + +
311J ARG* 4.2 8.7 - - + -
312J ARG* 4.3 28.9 - - + +
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Residues in contact with TRP 115 (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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1333I LEU* 3.6 30.3 - - + -
1335I ILE* 4.6 14.4 - - + -
113J HIS* 3.2 26.0 + + + +
114J ILE* 1.3 81.0 - - + +
116J PHE* 1.3 62.4 + - + +
118J LYS 5.2 1.1 - - - -
119J SER* 3.3 30.3 + - - -
307J LEU* 4.5 3.6 + - + -
308J ASP* 3.4 39.6 + - + +
311J ARG* 4.5 2.9 - - - +
328J ALA* 3.6 23.0 - - + +
331J ILE* 4.7 7.2 - - + -
1328J THR* 5.2 1.1 - - + -
1329J THR* 3.9 30.9 - - + +
1332J LEU* 4.0 32.5 - - + -
1333J THR* 3.6 27.4 - - + +
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Residues in contact with PHE 116 (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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1334I GLY 4.7 3.4 - - - -
1335I ILE* 3.6 26.9 - - + -
24J LEU* 3.6 22.0 - - + -
113J HIS* 3.3 45.9 + + + +
114J ILE 3.3 0.4 - - - -
115J TRP* 1.3 77.5 - - + +
117J LEU* 1.3 56.3 + - - +
119J SER* 4.8 0.4 - - - -
123J ARG* 3.4 16.7 + - + -
124J ILE* 3.3 40.2 + - + +
236J TRP 5.8 0.4 - - - -
237J MET* 4.2 22.2 - - + -
1333J THR* 4.3 19.5 - - + -
1336J ALA* 4.4 3.1 - - + -
1337J VAL* 3.6 32.1 - - + -
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Residues in contact with LEU 117 (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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112J ALA* 4.9 4.9 - - + -
113J HIS 3.2 14.3 + - - +
114J ILE* 3.8 12.6 - - + +
115J TRP 3.2 0.6 - - - -
116J PHE* 1.3 80.0 - - - +
118J LYS* 1.3 63.2 + - + +
119J SER 3.7 1.1 - - - -
122J SER* 2.8 27.3 + - - +
124J ILE* 4.2 13.7 - - + -
132J LEU* 3.5 11.8 - - + +
135J ILE* 3.7 30.7 - - + -
136J GLU* 4.3 20.9 - - + +
139J LEU* 3.8 23.6 - - + -
140J TYR* 5.3 5.2 - - + +
300J GLN* 5.9 0.7 - - - +
304J ASP* 5.7 2.7 - - - +
312J ARG* 4.4 12.8 - - - +
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Residues in contact with LYS 118 (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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10B C 4.7 11.5 + - - -
114J ILE* 2.9 20.0 + - + +
115J TRP* 3.9 2.9 - - - -
117J LEU* 1.3 87.9 - - + +
119J SER* 1.3 59.8 + - - +
120J LEU* 3.4 23.0 - - + +
132J LEU* 4.6 11.4 - - + +
136J GLU* 3.5 19.5 + - - +
311J ARG* 2.9 60.7 + - + +
312J ARG* 3.3 33.6 - - - +
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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