Contacts of the helix formed by residues 1113 - 1122 (chain A) in PDB entry 6KJV
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 PHE1113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1101A MET* 3.8 19.5 - - + -
1105A MET* 3.8 13.5 - - + -
1110A VAL* 3.1 31.6 + - - +
1111A ALA 3.2 0.2 - - - -
1112A GLY* 1.3 72.1 - - - +
1114A THR* 1.3 65.1 + - - +
1115A ASN* 3.2 3.6 - - - +
1116A SER* 3.1 14.6 + - - -
1117A LEU* 2.9 30.0 + - + +
1131A ASN* 6.0 0.4 - - - -
1132A LEU* 3.9 22.0 - - + -
1135A SER* 3.3 27.6 - - - -
1136A ARG* 3.4 42.8 - - - +
1137A TRP* 4.0 20.2 - + + -
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Residues in contact with THR1114 (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 ALA 4.0 9.5 + - - -
1112A GLY* 2.7 17.0 + - - -
1113A PHE* 1.3 70.0 - - - +
1115A ASN* 1.3 64.5 + - - +
1117A LEU* 3.3 6.4 + - - +
1118A ARG* 3.1 26.2 + - + +
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Residues in contact with ASN1115 (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 PHE 3.2 1.0 - - - -
1114A THR* 1.3 80.3 - - - +
1116A SER* 1.3 61.0 + - - +
1118A ARG* 3.9 4.3 + - - +
1119A MET* 3.2 33.9 + - - +
1131A ASN* 2.8 32.8 + - - +
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Residues in contact with SER1116 (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 PHE* 3.1 16.1 + - - +
1115A ASN* 1.3 76.7 - - - +
1117A LEU* 1.3 63.3 + - - +
1119A MET* 3.2 11.8 - - - +
1120A LEU* 2.9 34.6 + - - +
1128A ALA* 4.2 4.9 - - - +
1131A ASN* 2.6 25.7 + - - +
1132A LEU* 3.6 39.6 + - - +
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Residues in contact with LEU1117 (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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1082A LYS* 3.8 17.5 - - + +
1083A LEU* 3.7 32.3 - - + -
1086A VAL* 4.0 17.7 - - + +
1098A LEU* 4.5 13.5 - - + -
1110A VAL* 3.8 16.4 - - + +
1111A ALA* 4.0 14.1 - - - +
1113A PHE* 2.9 25.1 + - + +
1114A THR* 3.8 6.1 - - - +
1116A SER* 1.3 77.0 - - - +
1118A ARG* 1.3 62.9 + - - +
1120A LEU* 3.2 16.2 + - + +
1121A GLN* 3.0 24.1 + - - +
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Residues in contact with ARG1118 (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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1114A THR* 3.1 19.0 + - + +
1115A ASN* 4.2 6.3 - - - +
1116A SER 3.2 0.2 - - - -
1117A LEU* 1.3 76.4 - - - +
1119A MET* 1.3 63.2 + - + +
1121A GLN* 3.2 30.7 + - - +
1122A GLN* 3.2 51.4 + - - +
1124A ARG* 5.7 1.6 - - - +
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Residues in contact with MET1119 (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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1115A ASN* 3.2 36.8 - - - +
1116A SER* 3.2 11.7 - - - +
1118A ARG* 1.3 75.5 - - + +
1120A LEU* 1.3 64.0 + - - +
1122A GLN* 3.5 12.4 + - - -
1124A ARG* 3.1 55.3 + - + +
1127A GLU* 3.5 30.7 - - + +
1128A ALA* 3.7 31.2 - - + -
1131A ASN* 4.1 11.7 - - - -
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Residues in contact with LEU1120 (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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1086A VAL* 4.0 14.1 - - + -
1089A SER* 4.9 0.7 + - - -
1090A LEU* 4.4 7.5 - - + +
1098A LEU* 5.6 2.2 - - + -
1101A MET* 6.5 0.2 - - - -
1116A SER* 2.9 26.1 + - - +
1117A LEU* 3.6 19.1 - - + +
1119A MET* 1.3 77.3 - - - +
1121A GLN* 1.3 62.6 + - - +
1122A GLN 3.1 1.1 + - - -
1123A LYS* 3.3 9.9 + - - +
1125A TRP* 3.4 43.7 - - + +
1128A ALA* 4.0 18.8 - - + -
1132A LEU* 5.1 7.4 - - + -
1152A PHE* 3.9 45.5 - - + -
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Residues in contact with GLN1121 (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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1085A PRO* 3.7 34.6 + - - +
1086A VAL* 4.0 13.1 + - + +
1089A SER* 3.8 25.9 + - - +
1117A LEU 3.0 12.7 + - - +
1118A ARG* 3.2 24.7 + - - +
1120A LEU* 1.3 77.2 - - - +
1122A GLN* 1.3 60.2 + - + +
1123A LYS* 3.3 12.4 + - - +
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Residues in contact with GLN1122 (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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1118A ARG* 3.2 55.7 + - - +
1119A MET* 3.5 9.2 + - - +
1120A LEU 3.1 1.6 - - - -
1121A GLN* 1.3 78.2 - - + +
1123A LYS* 1.3 65.0 + - - +
1124A ARG* 2.7 56.2 + - + +
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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