Contacts of the helix formed by residues 1113 - 1122 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101B MET* 3.8 21.5 - - + -
1105B MET* 3.8 13.0 - - + -
1110B VAL* 3.1 29.8 + - - +
1111B ALA 3.2 0.6 - - - -
1112B GLY* 1.3 73.0 - - - +
1114B THR* 1.3 63.4 + - - +
1115B ASN* 3.1 4.7 + - - +
1116B SER* 3.1 12.8 + - - -
1117B LEU* 3.0 32.7 + - + +
1132B LEU* 3.9 22.0 - - + -
1135B SER* 3.3 29.2 - - - -
1136B ARG* 3.4 40.4 - - - +
1137B TRP* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111B ALA 4.0 9.5 + - - -
1112B GLY* 2.6 17.6 + - - -
1113B PHE* 1.3 72.2 - - - +
1115B ASN* 1.3 63.6 + - - +
1116B SER 3.5 0.2 + - - -
1117B LEU* 4.4 6.3 - - - +
1118B ARG* 3.6 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113B PHE 3.1 1.2 - - - -
1114B THR* 1.3 81.7 - - - +
1116B SER* 1.3 61.1 + - - +
1118B ARG* 4.0 3.2 + - - +
1119B MET* 3.3 32.8 + - - +
1131B ASN* 2.8 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113B PHE* 3.1 15.2 + - - -
1115B ASN* 1.3 76.4 - - - +
1117B LEU* 1.3 62.5 + - - +
1118B ARG 3.2 0.7 - - - -
1119B MET* 3.2 12.3 - - - +
1120B LEU* 2.9 33.6 + - - +
1128B ALA* 4.1 4.9 - - - +
1131B ASN* 2.6 25.8 + - - +
1132B LEU* 3.5 41.4 + - - +
1135B SER* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082B LYS* 3.9 17.0 - - + +
1083B LEU* 3.8 31.0 - - + -
1086B VAL* 4.0 15.6 - - + +
1098B LEU* 4.4 17.5 - - + -
1101B MET* 6.4 0.9 - - + -
1110B VAL* 3.8 16.6 - - + +
1111B ALA* 4.0 13.7 - - - +
1113B PHE* 3.0 26.1 + - + +
1114B THR* 4.4 4.7 - - - +
1116B SER* 1.3 77.5 - - - +
1118B ARG* 1.3 61.5 + - - +
1120B LEU* 3.2 16.1 + - + +
1121B GLN* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1114B THR* 3.6 15.5 + - + +
1115B ASN* 4.2 5.2 - - - +
1116B SER 3.2 0.4 - - - -
1117B LEU* 1.3 79.0 - - - +
1119B MET* 1.3 59.8 + - + +
1121B GLN* 3.2 25.4 + - - +
1122B GLN* 3.1 64.6 + - - +
1124B ARG* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115B ASN* 3.3 31.9 - - - +
1116B SER* 3.2 16.4 - - - +
1118B ARG* 1.3 75.1 - - + +
1120B LEU* 1.3 62.5 + - - +
1122B GLN* 3.5 12.3 + - - -
1124B ARG* 3.1 58.2 + - + +
1127B GLU* 3.5 31.9 - - + +
1128B ALA* 3.7 30.3 - - + -
1131B ASN* 4.1 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086B VAL* 4.1 13.5 - - + -
1089B SER* 5.0 0.5 + - - -
1090B LEU* 4.4 6.8 - - + +
1098B LEU* 5.5 1.3 - - + -
1101B MET* 6.4 0.2 - - - -
1116B SER* 2.9 20.5 + - - +
1117B LEU* 3.5 24.7 - - + +
1119B MET* 1.3 74.8 - - - +
1121B GLN* 1.3 64.3 + - - +
1122B GLN 3.1 1.1 + - - -
1123B LYS* 3.3 10.0 + - - +
1125B TRP* 3.3 45.1 - - + +
1128B ALA* 4.0 18.4 - - + -
1132B LEU* 5.0 8.7 - - + -
1152B PHE* 3.9 47.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085B PRO* 3.8 34.0 + - - +
1086B VAL* 4.0 12.9 + - + +
1089B SER* 3.8 26.1 + - - +
1117B LEU 2.9 13.1 + - - +
1118B ARG* 3.2 26.3 + - - +
1120B LEU* 1.3 76.5 - - - +
1122B GLN* 1.3 59.1 + - + +
1123B LYS* 3.3 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118B ARG* 3.1 56.0 + - - +
1119B MET* 4.0 9.5 - - - +
1120B LEU 3.1 1.6 - - - -
1121B GLN* 1.3 78.4 - - + +
1123B LYS* 1.3 64.8 + - - +
1124B ARG* 2.8 54.8 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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