Contacts of the helix formed by residues 1220 - 1228 (chain D) in PDB entry 6VVT
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 SER1220 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1218D THR* 3.1 26.9 + - - +
1219D ASP* 1.3 77.2 - - - +
1221D TRP* 1.3 58.5 + - - +
1223D SER* 3.1 17.3 + - - -
1224D ALA* 3.2 12.0 + - - +
1244D ASP* 2.1 30.8 + - - -
1251D GLU* 2.8 38.1 + - - +
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Residues in contact with TRP1221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116C LEU* 6.3 0.7 - - + -
1119C LEU* 4.6 20.0 - - + -
1126C VAL* 5.1 3.4 - - + -
10D LEU* 2.9 54.8 + - + -
11D ARG 4.3 2.7 - - - -
12D ILE* 3.2 46.0 - - + +
1218D THR 5.4 0.2 - - - -
1219D ASP 3.7 3.7 + - - +
1220D SER* 1.3 69.6 - - - +
1222D LEU* 1.3 84.2 + - + +
1223D SER 3.2 1.3 - - - -
1224D ALA* 3.3 4.3 + - - -
1225D ALA* 2.7 35.9 + - + +
1233D VAL* 3.6 9.0 - - + +
1234D LEU* 4.5 18.2 - - + -
1237D ALA* 4.0 16.8 - - + -
1242D ARG* 3.8 25.1 + - + -
1243D SER 4.2 1.8 - - - -
1244D ASP* 3.2 24.2 + - + +
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Residues in contact with LEU1222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112C PHE* 4.6 7.0 - - + -
1115C LEU* 5.3 7.2 - - + -
10D LEU* 3.6 25.6 - - + -
1220D SER* 3.3 6.5 - - - +
1221D TRP* 1.3 99.3 - - + +
1223D SER* 1.3 65.0 + - - +
1225D ALA* 3.8 6.9 - - + +
1226D SER* 3.1 23.0 + - - -
1244D ASP* 2.8 41.5 - - + +
1246D LEU* 4.7 1.6 - - + -
1251D GLU* 3.5 16.4 - - + -
1254D ILE* 4.3 31.6 - - + +
1255D ILE* 4.7 6.5 - - + -
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Residues in contact with SER1223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881D GLN* 4.0 14.6 + - - -
882D ASP* 5.4 2.9 + - - -
1218D THR* 4.4 5.5 + - - +
1220D SER* 3.1 31.1 + - - -
1221D TRP 3.2 0.2 - - - -
1222D LEU* 1.3 79.0 - - - +
1224D ALA* 1.3 61.1 + - - +
1226D SER* 2.6 23.4 + - - -
1227D PHE* 3.3 19.0 + - - -
1250D LYS* 4.0 17.2 - - - +
1251D GLU* 3.8 14.8 + - - -
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Residues in contact with ALA1224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1216D LEU* 4.1 23.8 - - - +
1218D THR* 3.9 13.0 - - + +
1220D SER 3.2 17.5 + - - +
1221D TRP* 3.8 3.6 - - - +
1223D SER* 1.3 77.0 + - - +
1225D ALA* 1.3 66.6 + - - +
1227D PHE* 3.2 26.0 + - - +
1228D GLN 3.7 10.4 + - - +
1233D VAL* 3.9 19.2 - - + +
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Residues in contact with ALA1225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413D PHE* 6.2 0.2 - - - -
1221D TRP* 2.7 22.3 + - + +
1222D LEU* 3.8 9.4 - - - +
1224D ALA* 1.3 75.0 - - - +
1226D SER* 1.3 60.8 + - - +
1227D PHE 3.4 0.5 + - - -
1228D GLN 4.3 3.5 + - - +
1230D THR* 2.8 36.7 + - + +
1233D VAL* 3.7 12.3 - - + +
1234D LEU* 3.4 31.6 - - + -
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Residues in contact with SER1226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413D PHE* 4.3 22.6 - - - +
414D ARG* 3.5 15.9 - - - +
874D ARG* 3.3 10.8 + - - -
1222D LEU 3.1 14.9 + - - -
1223D SER 2.6 21.0 + - - -
1225D ALA* 1.3 75.1 - - - +
1227D PHE* 1.3 68.5 + - - +
1230D THR* 4.9 1.1 + - - -
1250D LYS* 3.4 25.7 + - - +
1254D ILE* 4.5 12.3 - - - -
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Residues in contact with PHE1227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414D ARG* 4.3 4.9 - - - +
874D ARG* 2.9 25.9 + - + +
878D ASP* 3.0 51.1 - - + -
881D GLN* 3.2 19.7 - - - -
1215D SER* 3.9 28.7 - - - +
1216D LEU* 4.3 6.7 - - + -
1218D THR* 5.0 3.4 - - + -
1223D SER* 3.6 17.5 - - - -
1224D ALA* 3.2 15.7 + - - +
1225D ALA 4.3 0.2 - - - -
1226D SER* 1.3 83.3 + - - +
1228D GLN* 1.3 69.7 - - + +
1250D LYS* 3.1 33.4 - - - -
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Residues in contact with GLN1228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871D TYR* 3.6 29.7 + - - -
874D ARG* 4.8 8.0 - - - +
875D ARG* 5.5 3.9 - - + +
1212D THR* 3.7 25.3 - - + +
1216D LEU* 4.1 21.1 - - + +
1224D ALA 3.7 10.6 + - - +
1225D ALA 4.3 1.5 - - - +
1227D PHE* 1.3 86.9 - - + +
1229D GLU* 1.3 75.5 + - + +
1230D THR* 3.7 1.3 - - - -
1233D VAL* 3.8 5.2 - - - +
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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