Contacts of the helix formed by residues 1331 - 1340 (chain A) in PDB entry 3GTL
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 SER1331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1111A MET* 3.9 24.3 - - - -
1114A PRO* 5.4 0.4 - - - -
1311A VAL* 4.8 4.9 - - - -
1329A THR* 3.1 18.5 - - - +
1330A ASN* 1.3 79.1 + - - +
1332A PHE* 1.3 59.4 + - - +
1333A ILE* 3.2 14.4 + - - +
1334A ASP* 2.9 33.8 + - - +
1335A ILE* 3.1 25.6 + - - +
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Residues in contact with PHE1332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100A ARG* 4.6 8.7 - - - -
1104A ILE* 3.5 49.4 - - + -
1107A VAL* 4.0 16.8 - - + -
1108A ALA 5.0 4.3 - - - -
1111A MET* 6.5 0.4 - - - -
1330A ASN 3.3 3.7 + - - +
1331A SER* 1.3 72.7 - - - +
1333A ILE* 1.3 63.6 + - + +
1334A ASP 3.6 0.4 - - - -
1335A ILE* 4.0 10.1 - - - +
1336A MET* 3.3 23.4 + - - +
1344A GLY* 4.6 4.7 - - - +
1347A ALA* 3.9 8.3 - - + -
1348A LEU* 3.3 57.4 - - + +
1351A GLU* 4.3 15.7 - - + +
1381A LEU* 3.7 23.0 - - + +
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Residues in contact with ILE1333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107A VAL* 3.8 28.0 - - + -
1108A ALA 5.0 12.3 - - - +
1109A LYS* 4.7 31.6 - - + +
1111A MET* 6.2 1.6 - - - -
1331A SER* 3.2 10.0 - - - +
1332A PHE* 1.3 84.8 - - + +
1334A ASP* 1.3 72.5 + - - +
1336A MET* 3.6 9.4 + - + +
1337A GLU* 3.4 29.5 + - + +
1381A LEU* 4.1 11.2 - - + -
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Residues in contact with ASP1334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1311A VAL* 3.1 33.5 - - + +
1312A ASN* 5.5 0.8 - - - -
1313A LEU* 4.5 13.5 - - + -
1329A THR* 5.0 1.6 - - + -
1331A SER* 2.9 23.2 + - - +
1333A ILE* 1.3 80.7 - - - +
1335A ILE* 1.3 65.2 + - - +
1336A MET 3.1 1.1 - - - -
1337A GLU* 3.1 23.7 + - - +
1338A VAL* 3.0 27.4 + - + +
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Residues in contact with ILE1335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313A LEU* 4.2 21.3 - - + +
1327A ILE 5.3 4.9 - - - +
1328A TYR* 4.6 5.2 - - + -
1329A THR* 3.8 22.2 - - - +
1331A SER 3.1 20.6 + - - +
1332A PHE* 4.0 8.5 - - - +
1334A ASP* 1.3 75.4 - - - +
1336A MET* 1.3 59.8 + - - +
1339A LEU* 2.9 40.5 + - + +
1340A GLY 3.6 2.4 + - - -
1343A ALA* 4.2 11.2 - - + -
1344A GLY* 4.0 15.7 + - - +
1347A ALA* 3.9 21.1 - - + -
147E HIS* 5.4 0.7 - - + +
149E LEU* 4.2 17.9 - - + -
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Residues in contact with MET1336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332A PHE 3.3 17.4 + - - +
1333A ILE* 3.7 15.0 - - + +
1334A ASP 3.1 0.6 - - - -
1335A ILE* 1.3 79.2 - - - +
1337A GLU* 1.3 64.3 + - - +
1340A GLY* 3.2 23.4 + - - +
1341A ILE* 3.7 27.4 - - + +
1344A GLY* 4.4 12.3 - - - -
1380A GLY* 3.4 41.5 - - - -
1381A LEU* 3.5 22.7 - - + +
179E GLN* 6.3 0.4 - - + -
182E ASP* 5.3 2.2 - - - +
183E PRO* 4.2 3.3 - - - +
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Residues in contact with GLU1337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109A LYS* 5.3 8.4 + - - -
1333A ILE* 3.4 18.1 + - + +
1334A ASP* 3.1 29.0 + - - +
1336A MET* 1.3 83.2 - - - +
1338A VAL* 1.3 60.4 + - + +
183E PRO* 3.2 18.1 - - - +
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Residues in contact with VAL1338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313A LEU* 4.0 32.3 - - + -
1314A SER* 4.0 22.9 - - - +
1317A MET* 3.8 29.4 - - + -
1334A ASP* 3.0 19.6 + - + +
1337A GLU* 1.3 82.0 - - + +
1339A LEU* 1.3 72.2 + - + +
1340A GLY 3.4 1.3 - - - -
144E ILE* 4.0 11.6 - - + +
183E PRO* 3.2 18.5 - - - +
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Residues in contact with LEU1339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313A LEU* 5.3 2.9 - - + -
1317A MET* 5.0 6.7 - - - -
1335A ILE* 2.9 30.0 + - + +
1338A VAL* 1.3 87.7 - - + +
1340A GLY* 1.3 66.7 + - - +
1343A ALA* 3.7 20.5 - - + +
144E ILE* 4.0 25.2 - - + +
147E HIS* 3.1 53.4 - - + +
149E LEU* 4.5 2.5 - - + -
150E VAL* 3.9 16.7 - - + +
183E PRO* 4.1 3.8 - - - -
184E VAL* 4.1 16.8 - - - +
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Residues in contact with GLY1340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335A ILE 3.6 1.6 + - - -
1336A MET 3.2 18.5 + - - -
1338A VAL 3.4 2.6 - - - -
1339A LEU* 1.3 84.4 - - - +
1341A ILE* 1.3 54.3 + - - -
1342A GLU* 2.6 20.0 + - - +
1343A ALA 3.0 9.4 + - - -
1344A GLY 3.9 3.3 + - - -
150E VAL* 5.6 0.2 - - - +
153E HIS* 5.8 1.0 + - - -
182E ASP* 3.3 20.0 - - - -
183E PRO* 3.6 11.2 - - - -
184E VAL* 4.8 2.0 - - - +
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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