Contacts of the helix formed by residues 1140 - 1149 (chain U) 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 ARG1140 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139U ALA* 1.3 77.4 - - - +
1141U ALA* 1.3 65.4 + - - +
1142U SER* 3.9 12.8 - - - +
1143U LEU* 3.2 12.9 + - + +
1144U CYS* 3.0 20.7 + - - +
1160U VAL 5.7 0.2 - - - -
1166U PHE* 4.3 27.5 - - + +
1176U ASP* 6.2 3.8 - - + -
1298U ARG 3.1 14.7 + - - +
1299U LEU* 5.3 7.4 - - - +
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Residues in contact with ALA1141 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139U ALA 3.6 1.6 + - - -
1140U ARG* 1.3 73.2 - - - +
1142U SER* 1.3 62.6 + - - +
1144U CYS* 3.2 17.5 + - - +
1145U ASN* 3.2 12.8 + - - +
1156U ASN* 4.8 18.2 - - + -
1160U VAL* 5.3 10.1 + - - +
1161U GLN* 6.0 3.4 - - - -
1166U PHE* 5.8 0.2 - - - +
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Residues in contact with SER1142 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140U ARG* 3.1 8.2 - - - +
1141U ALA* 1.3 81.1 - - - +
1143U LEU* 1.3 60.5 + - - +
1145U ASN* 3.5 17.3 + - - +
1146U LEU* 4.2 2.4 + - - +
1176U ASP* 5.7 9.0 - - - -
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Residues in contact with LEU1143 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139U ALA* 4.7 3.4 - - + -
1140U ARG* 3.2 20.3 + - + +
1142U SER* 1.3 75.8 - - - +
1144U CYS* 1.3 66.1 + - - +
1145U ASN 3.1 0.4 - - - -
1146U LEU* 3.0 23.3 + - - +
1147U TYR* 4.2 1.2 + - - +
1294U MET 4.2 12.7 - - - +
1297U ALA* 4.5 19.3 - - + +
1298U ARG 5.2 2.0 - - - +
1299U LEU 6.1 2.7 - - - -
1301U LEU* 5.9 5.8 - - + -
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Residues in contact with CYS1144 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136U GLN* 5.8 8.3 - - + -
1139U ALA* 5.3 6.5 - - + +
1140U ARG 3.0 13.1 + - - +
1141U ALA* 3.2 15.0 + - - +
1143U LEU* 1.3 78.2 - - - +
1145U ASN* 1.3 56.8 + - - +
1147U TYR* 3.1 4.5 + - - +
1148U ASN* 2.8 35.8 + - + +
1155U GLY 5.5 6.7 - - - +
1156U ASN* 5.9 3.6 - - + -
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Residues in contact with ASN1145 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141U ALA 3.2 11.0 + - - +
1142U SER* 3.6 13.9 - - - +
1143U LEU 3.1 0.6 - - - -
1144U CYS* 1.3 76.2 - - - +
1146U LEU* 1.3 60.3 + - - +
1147U TYR* 3.0 1.8 + - - -
1148U ASN* 3.9 9.8 + - - +
1149U TRP* 4.4 9.9 + - - +
1318U PRO 5.3 3.8 - - - +
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Residues in contact with LEU1146 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142U SER 4.2 1.5 + - - +
1143U LEU* 3.0 17.8 + - - +
1145U ASN* 1.3 78.8 - - - +
1147U TYR* 1.3 59.8 + - - +
1149U TRP* 6.1 0.7 - - - -
1294U MET* 3.8 25.2 - - + +
1319U ALA* 4.0 26.9 - - + +
1322U GLN* 5.6 6.7 - - + -
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Residues in contact with TYR1147 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143U LEU 4.2 0.9 + - - +
1144U CYS* 3.1 5.5 + - - +
1146U LEU* 1.3 83.1 - - - +
1148U ASN* 1.3 61.0 + - - +
1149U TRP* 3.1 7.4 - - - -
1150U ARG* 3.1 23.4 + - - +
1151U TYR* 4.3 1.4 + - - +
1291U VAL* 4.3 22.8 - - + +
1294U MET* 4.2 15.5 - - + +
1295U SER* 4.9 8.7 - - - -
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Residues in contact with ASN1148 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144U CYS* 2.8 25.8 + - + +
1145U ASN* 3.9 5.5 + - - -
1147U TYR* 1.3 72.4 - - - +
1149U TRP* 1.3 64.2 + - - +
1150U ARG 3.1 3.2 + - - -
1151U TYR* 3.3 20.8 + - - +
1154U LEU* 3.4 39.3 + - + +
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Residues in contact with TRP1149 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145U ASN 4.4 10.5 + - - +
1146U LEU 6.1 0.2 - - - -
1147U TYR* 3.1 2.0 - - - -
1148U ASN* 1.3 77.6 - - - +
1150U ARG* 1.3 62.2 + - - +
1151U TYR 3.2 5.5 + - - +
1318U PRO* 4.6 24.7 - - + +
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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