Contacts of the helix formed by residues 1229 - 1241 (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 GLU1229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386D ARG* 4.1 7.5 + - - -
407D LYS* 5.2 9.1 - - - +
1228D GLN* 1.3 81.5 - - + +
1230D THR* 1.3 64.3 + - - +
1231D THR* 2.8 39.3 + - - -
1232D ARG* 4.1 18.5 - - + +
1233D VAL* 3.3 16.0 + - + +
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Residues in contact with THR1230 (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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406D LEU* 4.6 12.1 - - + -
407D LYS* 4.1 28.1 - - - +
413D PHE* 4.5 9.4 - - + +
1225D ALA* 2.8 33.1 + - + +
1226D SER 5.2 0.2 - - - -
1228D GLN 5.1 0.2 - - - -
1229D GLU* 1.3 73.3 + - - +
1231D THR* 1.3 60.9 + - - +
1233D VAL 3.6 0.2 + - - -
1234D LEU* 2.8 59.5 + - + +
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Residues in contact with THR1231 (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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105D TRP* 3.8 38.3 + - + +
109D GLY* 5.7 1.3 - - - -
383D ASP* 4.2 3.5 + - - -
386D ARG* 3.1 38.3 + - - +
407D LYS* 4.2 13.0 - - - +
1229D GLU* 2.8 20.0 + - - -
1230D THR* 1.3 79.0 - - - +
1232D ARG* 1.3 53.0 + - - +
1234D LEU* 3.1 5.1 + - - +
1235D THR* 2.7 43.9 + - + +
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Residues in contact with ARG1232 (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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110D VAL 4.3 9.6 - - - +
111D PRO* 3.7 16.5 - - - +
113D ARG* 2.9 29.4 - - - +
297D LYS* 5.6 8.1 - - - +
1229D GLU* 3.7 19.1 + - + +
1230D THR 3.5 0.2 - - - -
1231D THR* 1.3 79.7 - - - +
1233D VAL* 1.3 62.2 + - + +
1235D THR* 2.8 20.1 + - - -
1236D ASP* 2.8 54.1 + - - +
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Residues in contact with VAL1233 (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* 4.7 11.0 - - + +
1221D TRP* 3.6 31.4 - - + +
1224D ALA* 3.9 20.4 - - + +
1225D ALA* 3.7 12.6 - - + +
1228D GLN 3.8 10.1 - - - +
1229D GLU 3.3 17.0 - - - +
1230D THR 3.6 4.9 + - - +
1231D THR 3.3 0.6 - - - -
1232D ARG* 1.3 78.7 - - + +
1234D LEU* 1.3 55.0 + - + +
1236D ASP* 4.0 3.7 - - - +
1237D ALA* 2.7 37.9 + - + +
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Residues in contact with LEU1234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119C LEU* 3.9 7.0 - - + -
1124C LEU* 3.8 18.3 - - + +
12D ILE* 4.7 3.9 - - + +
105D TRP* 3.8 25.6 - - + -
406D LEU* 3.6 23.3 - - + -
1221D TRP* 4.5 19.3 - - + -
1225D ALA* 3.4 31.6 - - + -
1230D THR* 2.8 33.3 + - + +
1231D THR 3.6 2.7 - - - +
1233D VAL* 1.3 78.1 - - - +
1235D THR* 1.3 57.8 + - - +
1237D ALA* 3.8 3.0 - - - +
1238D ALA* 2.8 32.7 + - - +
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Residues in contact with THR1235 (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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1124C LEU* 5.6 0.2 - - - -
105D TRP* 3.7 48.7 - - + +
106D TYR* 4.4 16.8 - - + -
113D ARG* 3.5 18.7 + - - -
1231D THR* 2.7 29.3 + - + +
1232D ARG* 2.8 24.6 + - - -
1234D LEU* 1.3 73.1 - - - +
1236D ASP* 1.3 63.6 + - - -
1238D ALA* 3.2 3.6 + - - +
1239D ILE* 3.0 30.0 + - - +
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Residues in contact with ASP1236 (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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113D ARG* 3.0 28.0 + - - -
297D LYS* 6.4 2.0 - - - -
1232D ARG* 2.8 60.7 + - - +
1233D VAL* 4.1 3.5 - - - +
1235D THR* 1.3 74.1 + - - +
1237D ALA* 1.3 58.6 + - - +
1239D ILE* 4.0 5.4 - - - +
1240D ASN* 2.9 44.6 + - - +
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Residues in contact with ALA1237 (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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12D ILE* 3.2 27.5 - - + +
1221D TRP* 4.0 20.4 - - + -
1233D VAL* 2.7 27.1 + - + +
1234D LEU* 3.8 1.8 - - - +
1236D ASP* 1.3 71.7 - - - +
1238D ALA* 1.3 60.4 + - - +
1241D CYS* 2.8 25.1 + - - -
1242D ARG* 3.2 22.6 + - + +
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Residues in contact with ALA1238 (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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1124C LEU* 3.7 23.6 - - + -
12D ILE* 4.1 4.4 - - + +
13D GLY* 3.5 24.6 - - - +
14D LEU* 3.6 19.3 - - + +
106D TYR* 4.0 2.2 - - - +
307D ASN* 3.2 18.9 + - - -
1234D LEU 2.8 22.1 + - - +
1235D THR 3.7 2.9 - - - +
1237D ALA* 1.3 72.7 - - - +
1239D ILE* 1.3 62.3 + - - +
1241D CYS 3.3 4.2 + - - -
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Residues in contact with ILE1239 (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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14D LEU* 4.0 9.6 - - + -
106D TYR* 3.9 16.4 - - + -
113D ARG* 3.8 34.3 - - + +
298D VAL* 4.6 9.0 - - + +
301D ALA* 3.8 20.5 - - + +
302D PHE* 3.6 26.0 + - + -
305D SER* 3.8 9.9 + - - -
307D ASN* 3.4 12.1 + - - +
312D MET* 3.8 20.2 - - + -
1235D THR 3.0 21.7 + - - +
1236D ASP* 4.0 5.8 - - - +
1238D ALA* 1.3 73.8 - - - +
1240D ASN* 1.3 64.4 + - - +
1241D CYS 3.0 5.3 + - - -
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Residues in contact with ASN1240 (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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297D LYS* 5.0 12.3 - - - +
301D ALA* 3.2 27.7 - - - +
304D GLN* 4.9 11.2 - - - +
305D SER* 4.2 7.8 - - - -
1236D ASP* 2.9 33.9 + - - +
1239D ILE* 1.3 76.0 - - - +
1241D CYS* 1.3 68.5 + - - +
1242D ARG* 3.4 30.6 + - + +
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Residues in contact with CYS1241 (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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11D ARG* 3.9 20.2 - - - +
12D ILE 3.7 20.9 - - - -
13D GLY* 4.8 0.2 - - - -
305D SER* 4.0 13.7 - - - -
306D GLY 5.8 1.3 - - - -
307D ASN* 3.4 26.7 - - - +
1237D ALA 2.8 10.2 + - - -
1238D ALA 3.6 5.4 - - - -
1239D ILE 3.0 3.4 - - - -
1240D ASN* 1.3 80.0 - - - +
1242D ARG* 1.3 67.4 + - - +
1243D SER* 3.7 1.2 + - - -
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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