Contacts of the helix formed by residues 1242 - 1251 (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 GLY1242 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1237u LEU 4.2 4.2 - - - +
1238u ARG 3.1 15.1 + - - +
1239u VAL* 3.7 8.0 + - - -
1240u ALA 3.3 4.2 + - - -
1241u ILE* 1.3 81.4 - - - +
1243u PRO* 1.3 63.9 - - - +
1244u CYS* 3.1 6.1 + - - -
1245u ARG* 3.7 8.3 + - - +
1246u MET* 3.9 6.8 + - - +
1167v TYR 5.0 4.5 - - - -
1168v PHE* 5.4 1.3 - - - -
1169v PRO* 4.9 11.9 - - - -
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Residues in contact with PRO1243 (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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1238u ARG* 3.2 12.9 - - + +
1242u GLY* 1.3 71.2 - - - +
1244u CYS* 1.3 58.5 + - - +
1245u ARG 3.4 0.2 - - - -
1246u MET* 3.5 9.4 + - + +
1247u LEU* 2.9 29.5 + - - +
1272u ILE* 6.1 4.5 - - + +
1276u SER* 5.0 13.5 - - - +
1279u ALA* 4.4 28.5 - - + +
1280u LEU* 5.0 6.5 - - + +
1283u HIS* 5.1 1.7 - - - +
1167v TYR 4.7 6.2 - - - +
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Residues in contact with CYS1244 (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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1241u ILE 5.9 0.4 - - - +
1242u GLY* 3.1 3.2 - - - -
1243u PRO* 1.3 78.0 - - - +
1245u ARG* 1.3 58.9 + - - +
1247u LEU* 3.3 2.6 + - - +
1248u GLN* 2.9 29.0 + - - +
1283u HIS* 4.2 24.4 - - + +
1029v TYR* 5.6 11.7 - - + -
1030v PRO 5.9 4.0 - - - +
1167v TYR 5.5 2.3 + - - +
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Residues in contact with ARG1245 (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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5878 HIS* 6.1 5.4 - - + -
1241u ILE* 4.8 18.3 + - + +
1242u GLY* 3.7 8.2 + - - +
1243u PRO 3.4 0.2 - - - -
1244u CYS* 1.3 75.4 - - - +
1246u MET* 1.3 59.7 + - - +
1248u GLN* 3.4 7.5 + - - +
1249u TYR* 2.9 29.1 + - - +
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Residues in contact with MET1246 (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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1234u LEU 5.8 1.8 - - - +
1237u LEU 5.4 1.3 - - - +
1238u ARG* 4.8 15.5 - - + +
1242u GLY 3.9 7.1 + - - +
1243u PRO* 3.5 14.8 + - + +
1244u CYS 3.3 0.6 - - - -
1245u ARG* 1.3 79.8 - - - +
1247u LEU* 1.3 57.7 + - - +
1249u TYR* 3.3 7.7 + - - +
1250u CYS* 2.9 26.9 + - - +
1272u ILE* 5.4 11.2 - - + -
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Residues in contact with LEU1247 (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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1243u PRO 2.9 18.7 + - - +
1244u CYS* 3.3 5.6 + - - +
1246u MET* 1.3 73.2 - - - +
1248u GLN* 1.3 60.6 + - - +
1250u CYS* 3.1 8.6 + - - +
1251u LEU* 3.0 28.4 + - - +
1280u LEU* 5.9 5.6 - - + -
1283u HIS* 5.0 15.9 - - + +
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Residues in contact with GLN1248 (chain u).
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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4968 ASN* 3.3 27.8 - - + +
4978 SER* 3.4 26.2 - - - +
4988 VAL 3.6 3.8 + - - -
1244u CYS 2.9 17.4 + - - +
1245u ARG* 3.7 7.6 - - - +
1247u LEU* 1.3 75.4 - - - +
1249u TYR* 1.3 61.8 + - - +
1251u LEU* 3.6 8.7 + - - +
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Residues in contact with TYR1249 (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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4988 VAL* 4.7 13.5 - - + +
1216u TRP* 5.8 8.3 - - + -
1245u ARG 2.9 17.6 + - - +
1246u MET* 3.6 8.3 - - - +
1247u LEU 3.2 0.2 - - - -
1248u GLN* 1.3 77.5 - - - +
1250u CYS* 1.3 60.3 + - - +
1251u LEU 3.7 5.7 - - - +
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Residues in contact with CYS1250 (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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1246u MET 2.9 13.4 + - - +
1247u LEU* 3.1 11.8 + - - +
1249u TYR* 1.3 75.3 - - - +
1251u LEU* 1.3 66.1 + - - +
1253u GLY* 3.4 17.5 + - - -
1254u LEU* 4.0 6.7 + - - +
1265u TYR* 5.1 12.7 - - + +
1268u ILE* 6.1 3.1 - - + -
1269u TYR* 5.1 18.2 - - + +
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Residues in contact with LEU1251 (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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4918 LEU* 5.0 7.6 - - + -
4978 SER* 3.9 13.0 - - - -
4988 VAL 3.7 12.5 - - - +
1247u LEU 3.0 14.6 + - - +
1248u GLN* 3.9 11.6 - - - +
1249u TYR 3.4 7.9 - - - +
1250u CYS* 1.3 81.7 - - - +
1252u GLN* 1.3 67.2 + - - +
1253u GLY* 3.2 0.5 + - - -
1254u LEU* 5.3 2.9 - - - +
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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