Contacts of the helix formed by residues 1329 - 1340 (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 ASN1329 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1306D PRO* 6.2 0.2 - - - -
1327D PHE 3.9 1.4 + - - -
1328D PHE* 1.3 73.9 - - - +
1330D PRO* 1.3 60.8 - - - +
1331D ILE 3.2 3.1 - - - -
1332D GLN* 2.9 7.8 + - - +
1333D THR 2.8 24.1 + - - -
1520D PRO* 6.2 3.6 - - - -
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Residues in contact with PRO1330 (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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1302D LEU 5.7 3.5 - - - +
1328D PHE 4.0 0.4 - - - -
1329D ASN* 1.3 69.7 - - - +
1331D ILE* 1.3 61.2 + - - +
1333D THR* 4.5 2.2 - - - +
1334D GLN* 2.9 20.4 + - - -
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Residues in contact with ILE1331 (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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1329D ASN 3.0 1.2 + - - -
1330D PRO* 1.3 74.0 - - - +
1332D GLN* 1.3 63.2 - - - +
1334D GLN* 3.0 4.0 + - - -
1335D VAL* 2.9 20.4 + - - -
1354D SER 5.6 3.8 - - - -
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Residues in contact with GLN1332 (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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1328D PHE* 5.6 1.3 - - - +
1329D ASN* 2.9 10.3 + - - +
1331D ILE* 1.3 75.1 - - - +
1333D THR* 1.3 56.8 + - - +
1335D VAL* 3.1 2.5 + - - +
1336D PHE* 2.8 29.8 + - - -
1354D SER 5.4 4.0 + - - -
1355D GLY 6.1 1.1 - - - -
1359D CYS* 6.1 4.7 - - - +
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Residues in contact with THR1333 (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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1307D LEU* 5.1 15.9 - - - +
1328D PHE* 5.0 2.8 - - - +
1329D ASN 2.8 19.0 + - - +
1330D PRO* 4.0 2.2 - - - -
1332D GLN* 1.3 71.7 - - - +
1334D GLN* 1.3 59.6 + - - +
1336D PHE* 3.7 8.7 + - - +
1337D ASN 4.8 2.4 + - - -
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Residues in contact with GLN1334 (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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1330D PRO 2.9 15.8 + - - -
1331D ILE 3.6 3.4 - - - -
1333D THR* 1.3 77.6 - - - +
1335D VAL* 1.3 59.7 + - - +
1337D ASN 4.9 1.6 + - - -
1338D THR 5.3 1.2 + - - -
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Residues in contact with VAL1335 (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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1331D ILE 2.9 13.2 + - - -
1332D GLN* 3.7 3.1 - - - +
1334D GLN* 1.3 76.4 - - - +
1336D PHE* 1.3 66.7 + - - +
1337D ASN 3.5 0.4 - - - -
1338D THR* 3.0 6.6 + - - -
1339D VAL* 2.9 20.4 + - - -
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Residues in contact with PHE1336 (chain D).
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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1332D GLN 2.8 15.8 + - - -
1333D THR* 3.7 5.7 + - - +
1334D GLN 3.3 2.6 - - - -
1335D VAL* 1.3 76.2 - - - +
1337D ASN* 1.3 56.8 + - - +
1339D VAL* 3.1 1.5 + - - +
1340D TYR* 2.7 35.3 + - - -
1341D ASN 3.9 0.2 + - - -
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Residues in contact with ASN1337 (chain D).
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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1333D THR 4.8 3.4 + - - -
1334D GLN 4.9 1.6 + - - -
1335D VAL 3.5 0.4 - - - -
1336D PHE* 1.3 73.6 - - - +
1338D THR* 1.3 61.9 + - - +
1341D ASN* 3.2 22.3 + - - +
1342D SER* 3.3 7.3 + - - -
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Residues in contact with THR1338 (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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1334D GLN 5.3 1.0 + - - -
1335D VAL 3.0 7.9 + - - -
1337D ASN* 1.3 79.5 - - - +
1339D VAL* 1.3 56.6 + - - +
1342D SER* 3.2 25.0 + - - +
1344D ASP 4.7 6.2 + - - +
1510D SER* 6.6 0.2 - - - +
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Residues in contact with VAL1339 (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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1335D VAL 2.9 13.6 + - - -
1336D PHE* 3.7 1.6 - - - +
1338D THR* 1.3 77.3 - - - +
1340D TYR* 1.3 59.9 + - - +
1342D SER 3.6 8.3 - - - +
1344D ASP 5.7 2.2 - - - -
1359D CYS 5.8 2.9 - - - -
1362D PHE* 5.1 1.1 - - - -
1363D ALA* 3.9 24.5 - - - +
1366D ARG* 5.9 0.5 - - - -
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Residues in contact with TYR1340 (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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1336D PHE* 2.7 17.7 + - - +
1339D VAL* 1.3 74.7 - - - +
1341D ASN* 1.3 59.3 + - - +
1342D SER 3.1 6.9 + - - +
1362D PHE* 4.7 14.4 - - - +
1366D ARG* 4.7 12.5 - - - +
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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