Contacts of the helix formed by residues 1136 - 1146 (chain r) in PDB entry 6FF7
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 PRO1136 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1134r LYS 3.9 1.6 - - - -
1135r LEU* 1.3 74.0 - - - +
1137r GLU* 1.3 63.1 + - - +
1138r GLU* 4.6 2.0 - - + +
1139r VAL* 3.8 19.9 - - + +
1140r VAL* 3.4 20.3 + - - +
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Residues in contact with GLU1137 (chain r).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1135r LEU 3.8 2.2 + - - -
1136r PRO* 1.3 69.7 - - - +
1138r GLU* 1.3 60.9 + - - +
1140r VAL* 3.3 6.8 + - - +
1141r LYS* 2.9 30.4 + - - +
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Residues in contact with GLU1138 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136r PRO* 3.4 2.5 - - + +
1137r GLU* 1.3 79.8 - - - +
1139r VAL* 1.3 56.3 + - - +
1141r LYS* 3.6 7.2 + - - +
1142r LYS* 2.9 29.2 + - - +
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Residues in contact with VAL1139 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135r LEU* 6.3 0.9 - - + -
1136r PRO* 3.6 22.3 + - + +
1137r GLU 3.2 0.4 - - - -
1138r GLU* 1.3 75.7 - - - +
1140r VAL* 1.3 65.3 + - - +
1142r LYS* 3.0 8.7 + - - +
1143r ILE* 2.9 23.2 + - - +
1170r MET* 5.6 10.8 - - + -
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Residues in contact with VAL1140 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127r CYS* 5.1 14.1 - - + +
1129r LEU* 5.7 6.1 - - + -
1130r ARG* 5.7 13.2 - - + +
1135r LEU* 5.7 5.6 - - + +
1136r PRO 3.4 10.5 + - - +
1137r GLU* 3.3 10.5 + - - +
1139r VAL* 1.3 78.4 - - - +
1141r LYS* 1.3 63.0 + - - +
1143r ILE* 3.1 8.2 + - - +
1144r GLU* 2.9 22.1 + - - +
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Residues in contact with LYS1141 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137r GLU 2.9 17.6 + - - +
1138r GLU* 3.8 7.9 - - - +
1140r VAL* 1.3 76.0 - - - +
1142r LYS* 1.3 56.7 + - - +
1144r GLU* 3.2 9.8 + - - +
1145r LYS* 2.9 27.5 + - - +
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Residues in contact with LYS1142 (chain r).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1138r GLU 2.9 19.1 + - - +
1139r VAL* 3.0 9.6 + - - +
1141r LYS* 1.3 74.5 - - - +
1143r ILE* 1.3 63.6 + - - +
1145r LYS* 3.2 22.0 - - - +
1146r LYS* 3.7 6.4 + - - +
1165r ILE* 4.4 23.6 - - + +
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Residues in contact with ILE1143 (chain r).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1139r VAL 2.9 12.3 + - - +
1140r VAL* 3.9 7.4 - - - +
1142r LYS* 1.3 77.1 - - - +
1144r GLU* 1.3 53.8 + - - +
1146r LYS* 2.7 26.3 - - - +
1148r PHE* 4.9 3.6 + - - +
1165r ILE* 4.9 9.6 - - + +
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Residues in contact with GLU1144 (chain r).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2311A PRO* 6.1 0.5 - - - +
2315A LEU* 5.6 11.1 - - + +
1126r MET* 6.4 0.7 - - - -
1127r CYS* 5.3 11.9 - - + +
1140r VAL 2.9 12.8 + - - +
1141r LYS* 3.5 13.5 - - - +
1142r LYS 3.2 0.2 - - - -
1143r ILE* 1.3 75.2 - - - +
1145r LYS* 1.3 66.4 + - - +
1146r LYS 3.6 5.1 - - - +
1147r ASN* 4.5 3.3 + - - +
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Residues in contact with LYS1145 (chain r).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1604A LEU 5.1 0.7 - - - +
1605A GLU* 3.9 21.9 - - + +
1606A ILE 6.1 2.0 - - - +
1607A GLU* 6.2 4.3 - - + -
1141r LYS 2.9 13.4 + - - +
1142r LYS* 3.2 16.5 + - - +
1144r GLU* 1.3 78.7 - - - +
1146r LYS* 1.3 59.7 + - - +
1147r ASN* 3.7 2.1 + - - +
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Residues in contact with LYS1146 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1605A GLU* 4.7 7.2 - - + +
1634A SER* 2.8 39.3 - - - -
1142r LYS 3.7 5.9 + - - +
1143r ILE* 2.7 28.9 - - - +
1144r GLU 3.6 2.6 - - - +
1145r LYS* 1.3 79.2 - - - +
1147r ASN* 1.3 61.7 + - - +
1148r PHE* 3.4 9.7 + - + +
1164r LEU* 5.9 3.1 - - + -
1165r ILE* 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