Contacts of the helix formed by residues 1331 - 1336 (chain A) in PDB entry 2H7C
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 THR1331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1258A LYS* 3.7 32.5 + - + +
1323A ILE* 3.8 16.5 - - + +
1330A LYS* 1.3 76.8 - - - +
1332A PRO* 1.3 75.6 - - - +
1333A GLU* 3.7 3.9 + - - +
1334A GLU* 3.0 39.2 + - - +
1335A LEU* 2.9 19.8 + - - +
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Residues in contact with PRO1332 (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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1229A VAL* 5.7 0.2 - - + -
1232A LEU* 4.0 16.8 - - + +
1250A ALA* 3.7 42.6 - - + +
1251A LEU* 4.3 5.2 - - + -
1256A VAL* 4.2 18.6 - - + -
1258A LYS* 4.4 0.9 - - - -
1323A ILE* 4.1 12.6 - - + -
1328A LEU* 4.6 13.7 - - + -
1330A LYS 4.2 0.2 - - - +
1331A THR* 1.3 87.2 - - - +
1333A GLU* 1.3 71.9 + - - +
1335A LEU* 3.8 3.7 - - + +
1336A GLN* 3.0 29.1 + - - +
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Residues in contact with GLU1333 (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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1250A ALA 4.9 1.0 - - - +
1251A LEU* 3.3 29.1 - - + +
1253A SER* 6.0 1.6 - - - -
1258A LYS* 2.6 38.3 + - - +
1331A THR* 3.1 5.6 - - - +
1332A PRO* 1.3 80.1 - - - +
1334A GLU* 1.3 60.6 + - + +
1336A GLN* 3.3 26.9 - - - +
1337A ALA* 4.2 5.4 + - - +
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Residues in contact with GLU1334 (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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1330A LYS* 4.0 32.0 + - + +
1331A THR* 3.0 31.5 + - - +
1333A GLU* 1.3 79.7 - - + +
1335A LEU* 1.3 62.8 + - - +
1337A ALA* 3.5 18.2 - - - +
1338A GLU* 4.3 1.9 + - - +
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Residues in contact with LEU1335 (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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1232A LEU* 4.1 32.9 - - + +
1328A LEU* 3.8 24.9 - - + -
1329A LEU* 4.6 9.0 - - + +
1330A LYS* 3.4 48.5 - - + +
1331A THR 2.9 16.2 + - - +
1332A PRO* 3.2 7.4 + - + +
1334A GLU* 1.3 74.7 - - - +
1336A GLN* 1.3 56.9 + - - +
1337A ALA 3.0 10.1 + - - -
1338A GLU* 3.0 28.5 + - + +
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Residues in contact with GLN1336 (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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1232A LEU* 4.5 15.5 - - + +
1251A LEU* 3.5 23.0 - - - +
1332A PRO 3.0 14.6 + - - +
1333A GLU* 3.3 25.2 - - - +
1335A LEU* 1.3 74.9 - - - +
1337A ALA* 1.3 51.1 + - - +
1338A GLU 3.3 1.6 - - - -
1339A ARG* 2.5 26.6 + - - -
1432A ILE* 4.0 3.8 - - - +
1433A VAL* 3.8 32.7 - - - +
1436A ASN* 3.5 40.5 + - + +
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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