Contacts of the helix formed by residues 1382 - 1397 (chain D) in PDB entry 6AH0
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 MET1382 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1380D THR* 3.2 8.3 - - - +
1381D PRO* 1.3 76.6 - - - +
1383D GLU* 1.3 61.1 + - - +
1384D ALA 3.2 3.6 - - - +
1385D LEU* 3.1 7.8 + - - +
1386D ALA* 2.8 25.6 + - - -
1428D THR* 6.1 0.2 - - - -
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Residues in contact with GLU1383 (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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1381D PRO 4.0 3.2 + - - -
1382D MET* 1.3 69.2 - - - +
1384D ALA* 1.3 64.2 + - - +
1386D ALA* 3.2 3.4 + - - +
1387D GLU* 3.0 20.1 + - - -
1428D THR* 6.0 4.7 - - - +
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Residues in contact with ALA1384 (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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1382D MET* 3.2 0.6 - - - +
1383D GLU* 1.3 75.0 - - - +
1385D LEU* 1.3 64.6 - - - +
1386D ALA 3.2 0.3 + - - -
1387D GLU* 3.2 3.2 + - - +
1388D GLN* 3.0 19.8 + - - -
1652D TRP 5.4 0.2 - - - -
1653D GLY* 4.5 21.2 - - - +
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Residues in contact with LEU1385 (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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1380D THR* 6.3 0.7 - - - -
1382D MET* 3.1 11.3 + - - +
1384D ALA* 1.3 74.2 - - - +
1386D ALA* 1.3 56.2 + - - +
1388D GLN* 3.2 4.4 + - - +
1389D VAL* 2.9 25.3 + - - -
1652D TRP* 4.7 13.8 + - - +
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Residues in contact with ALA1386 (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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1380D THR* 5.8 6.9 - - - +
1382D MET 2.8 13.9 + - - -
1383D GLU* 3.2 5.6 + - - +
1384D ALA 3.1 0.6 - - - -
1385D LEU* 1.3 72.5 - - - +
1387D GLU* 1.3 60.0 + - - +
1389D VAL* 3.0 3.6 + - - +
1390D TYR* 2.9 25.5 + - - -
1426D ILE 6.5 0.7 - - - -
1427D SER 6.1 4.3 - - - +
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Residues in contact with GLU1387 (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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1383D GLU 3.0 12.9 + - - -
1384D ALA* 3.8 2.5 - - - +
1386D ALA* 1.3 75.2 - - - +
1388D GLN* 1.3 56.4 + - - +
1390D TYR* 3.2 2.6 + - - +
1391D MET* 3.0 27.9 + - - -
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Residues in contact with GLN1388 (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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1384D ALA 3.0 13.7 + - - -
1385D LEU* 3.5 6.5 - - - +
1386D ALA 3.1 0.2 - - - -
1387D GLU* 1.3 77.2 - - - +
1389D VAL* 1.3 59.5 + - - +
1391D MET* 3.9 1.0 + - - -
1392D ASP* 3.8 11.1 + - - -
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Residues in contact with VAL1389 (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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1385D LEU 2.9 13.2 + - - -
1386D ALA* 3.0 3.3 + - - +
1388D GLN* 1.3 74.3 - - - +
1390D TYR* 1.3 61.3 + - - +
1392D ASP* 3.1 3.8 + - - -
1393D TRP* 2.9 27.0 + - - -
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Residues in contact with TYR1390 (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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1386D ALA 2.9 13.3 + - - -
1387D GLU* 3.2 4.2 + - - +
1389D VAL* 1.3 76.7 - - - +
1391D MET* 1.3 55.5 + - - +
1393D TRP* 4.5 1.3 - - - +
1394D TYR* 2.9 30.1 + - - +
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Residues in contact with MET1391 (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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1387D GLU 3.0 15.1 + - - -
1388D GLN* 4.4 2.2 - - - +
1389D VAL 3.3 0.2 - - - -
1390D TYR* 1.3 77.2 - - - +
1392D ASP* 1.3 61.3 + - - +
1394D TYR* 4.4 0.7 - - - +
1395D GLU* 3.8 9.4 + - - -
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Residues in contact with ASP1392 (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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1388D GLN 3.8 8.4 + - - -
1389D VAL 3.1 6.6 + - - -
1391D MET* 1.3 77.1 - - - +
1393D TRP* 1.3 58.9 + - - +
1395D GLU* 3.1 5.5 + - - -
1396D LYS* 2.9 24.3 + - - -
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Residues in contact with TRP1393 (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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1389D VAL 2.9 17.7 + - - -
1390D TYR* 3.9 1.8 - - - +
1392D ASP* 1.3 71.2 - - - +
1394D TYR* 1.3 56.8 + - - +
1396D LYS* 3.8 4.7 - - - +
1397D PHE* 2.9 26.3 + - - -
1398D GLN 3.9 0.9 + - - -
1405D VAL* 5.9 2.1 - - - -
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Residues in contact with TYR1394 (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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1390D TYR 2.9 17.3 + - - -
1391D MET 4.4 1.1 - - - -
1392D ASP 3.2 0.2 + - - -
1393D TRP* 1.3 78.1 - - - +
1395D GLU* 1.3 56.5 + - - +
1398D GLN* 3.1 10.5 + - - +
1399D ASP* 3.0 21.8 + - - -
1405D VAL* 5.7 9.0 - - - +
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Residues in contact with GLU1395 (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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1391D MET 3.8 7.1 + - - -
1392D ASP 3.1 6.8 + - - -
1394D TYR* 1.3 76.4 - - - +
1396D LYS* 1.3 63.9 + - - +
1397D PHE 3.2 0.9 + - - -
1399D ASP* 3.7 5.5 + - - +
1400D ARG* 3.4 19.9 + - - -
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Residues in contact with LYS1396 (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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1320D LEU* 6.1 2.5 - - - +
1392D ASP 2.9 15.0 + - - -
1393D TRP* 4.0 3.1 - - - +
1394D TYR 3.5 0.2 - - - -
1395D GLU* 1.3 77.9 - - - +
1397D PHE* 1.3 56.6 + - - +
1400D ARG* 4.6 2.9 + - - -
1401D LEU* 4.4 6.4 + - - -
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Residues in contact with PHE1397 (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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1393D TRP 2.9 14.4 + - - -
1396D LYS* 1.3 78.8 - - - +
1398D GLN* 1.3 58.5 + - - +
1399D ASP 3.3 1.1 - - - -
1401D LEU* 2.7 31.5 + - - +
1402D ASN 3.0 6.1 + - - -
1403D LYS* 3.5 7.2 + - - -
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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