Contacts of the helix formed by residues 1110 - 1117 (chain A) in PDB entry 6Q6Q
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 LEU1110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1032A ILE* 4.5 5.8 - - + -
1106A LEU* 3.2 22.2 + - + +
1107A LEU* 3.7 5.6 - - - +
1108A LYS 3.1 0.8 - - - -
1109A ARG* 1.3 79.4 - - + +
1111A GLU* 1.3 60.0 + - - +
1112A PRO 3.4 1.8 - - - -
1113A ILE* 3.1 19.4 + - + +
1114A ILE* 2.9 39.8 + - + +
1122A TRP* 3.6 35.7 - - + -
1125A TRP* 4.2 12.6 - - + +
1129A ALA* 3.7 29.8 - - + -
1134A ILE* 4.7 4.0 - - + -
1136A LEU* 4.1 18.4 - - + -
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Residues in contact with GLU1111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107A LEU 3.2 9.0 + - - +
1108A LYS* 3.1 41.5 + - - +
1110A LEU* 1.3 78.2 - - - +
1112A PRO* 1.3 70.2 - - + +
1114A ILE* 4.4 6.5 - - + +
1115A SER* 3.0 30.4 + - - -
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Residues in contact with PRO1112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108A LYS 3.9 4.7 - - - +
1109A ARG 3.7 12.6 - - - +
1110A LEU 3.6 2.9 - - - -
1111A GLU* 1.3 93.1 - - + +
1113A ILE* 1.3 64.6 + - + +
1115A SER* 3.2 16.6 + - - +
1116A LYS* 3.2 18.9 + - - +
1132A GLU* 5.7 2.0 - - - +
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Residues in contact with ILE1113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109A ARG 4.9 1.3 - - - +
1110A LEU* 3.1 20.9 + - + +
1112A PRO* 1.3 79.7 - - + +
1114A ILE* 1.3 65.6 + - + +
1116A LYS* 3.6 7.1 + - - +
1117A ASN* 3.3 23.5 + - + +
1125A TRP* 4.1 22.1 + - + +
1128A THR* 3.3 23.8 - - - +
1129A ALA* 3.6 36.3 - - + +
1132A GLU* 3.6 27.8 - - - +
1134A ILE* 4.0 11.7 - - + -
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Residues in contact with ILE1114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064A ARG* 5.3 11.2 - - - +
1107A LEU* 3.7 29.8 - - + +
1110A LEU* 2.9 31.9 + - + +
1111A GLU* 4.1 5.6 - - + +
1113A ILE* 1.3 76.5 - - + +
1115A SER* 1.3 60.6 + - - +
1117A ASN 3.1 0.5 - - - -
1118A PRO* 3.0 34.0 - - + +
1122A TRP* 4.7 4.7 - - + -
1125A TRP* 3.8 52.7 - - + +
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Residues in contact with SER1115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1111A GLU* 3.0 20.1 + - - -
1112A PRO* 3.2 13.3 + - - +
1114A ILE* 1.3 79.1 - - - +
1116A LYS* 1.3 63.2 + - - +
1117A ASN 3.1 1.4 + - - -
1118A PRO* 3.4 15.0 - - - +
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Residues in contact with LYS1116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112A PRO 3.2 17.3 + - - +
1113A ILE* 4.2 6.7 - - - +
1114A ILE 3.4 0.4 - - - -
1115A SER* 1.3 80.5 + - - +
1117A ASN* 1.3 60.7 + - + +
1118A PRO* 3.9 1.9 - - - +
1132A GLU* 4.0 19.2 + - - -
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Residues in contact with ASN1117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113A ILE* 3.3 12.3 + - + +
1114A ILE 3.1 3.5 - - - +
1115A SER 3.1 0.4 - - - -
1116A LYS* 1.3 81.0 - - + +
1118A PRO* 1.3 64.2 - - - +
1119A LYS* 3.3 7.6 + - - +
1120A GLY* 3.1 28.3 + - - -
1124A ASP* 4.0 12.1 + - - +
1125A TRP* 2.8 38.0 + - + +
1128A THR* 6.4 0.2 - - - +
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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