Contacts of the helix formed by residues 1336 - 1346 (chain A) in PDB entry 4C2A
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 ARG1336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1335A LYS* 1.3 73.8 - - - +
1337A PRO* 1.3 76.6 - - + +
1338A SER* 3.7 18.9 + - - +
1339A GLU* 2.9 50.9 + - + +
1340A LEU* 3.1 9.1 + - - +
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Residues in contact with PRO1337 (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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1304A MET* 5.0 0.2 - - - +
1309A VAL 3.4 24.2 - - - +
1310A SER* 3.8 20.6 - - - +
1335A LYS 3.6 4.0 - - - +
1336A ARG* 1.3 86.2 - - + +
1338A SER* 1.3 57.3 + - - +
1340A LEU* 3.0 16.5 + - + +
1341A ARG* 2.9 47.1 + - + +
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Residues in contact with SER1338 (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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1336A ARG* 3.2 23.5 + - - +
1337A PRO* 1.3 78.6 - - - +
1339A GLU* 1.3 61.9 + - - +
1341A ARG* 3.6 27.9 + - - +
1342A ARG* 3.0 27.0 + - - +
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Residues in contact with GLU1339 (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 LYS* 4.4 14.6 - - + -
1336A ARG* 2.9 56.1 + - + +
1338A SER* 1.3 83.1 + - - +
1340A LEU* 1.3 59.2 + - - +
1342A ARG* 2.9 45.0 + - - +
1343A ILE* 2.9 39.5 + - + +
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Residues in contact with LEU1340 (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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1304A MET* 3.8 14.1 - - + +
1309A VAL* 4.1 16.2 - - + -
1310A SER 4.8 0.2 - - - -
1311A GLN* 3.5 39.5 - - + +
1316A VAL* 4.7 0.7 - - + -
1329A ILE* 3.5 41.6 - - + +
1333A ASP* 5.1 1.8 - - + -
1335A LYS* 3.9 28.9 - - + +
1336A ARG 3.1 8.6 + - - +
1337A PRO* 3.0 21.5 + - + +
1339A GLU* 1.3 77.4 - - - +
1341A ARG* 1.3 60.4 + - - +
1343A ILE* 3.3 2.5 + - + -
1344A ALA* 3.0 21.5 + - - +
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Residues in contact with ARG1341 (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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1301A VAL* 3.7 19.4 - - + +
1304A MET* 4.0 24.9 - - + -
1305A GLU* 3.6 43.3 + - - +
1309A VAL* 5.4 1.5 + - + -
1337A PRO* 2.9 31.2 + - + +
1338A SER* 3.7 39.1 + - - +
1340A LEU* 1.3 71.8 - - - +
1342A ARG* 1.3 66.3 + - - +
1344A ALA* 3.4 1.1 + - - -
1345A SER* 3.0 23.7 + - - -
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Residues in contact with ARG1342 (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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1338A SER 3.0 18.1 + - - +
1339A GLU* 2.9 37.9 + - - +
1341A ARG* 1.3 77.2 - - - +
1343A ILE* 1.3 87.0 + - - +
1345A SER* 2.6 23.1 + - - +
1346A GLN* 2.7 57.8 + - - +
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Residues in contact with ILE1343 (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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1328A TYR* 3.9 27.9 - - + +
1329A ILE* 3.7 25.1 - - + -
1335A LYS* 3.7 38.8 - - + +
1339A GLU* 2.9 24.3 + - + +
1340A LEU* 3.6 7.9 - - + +
1342A ARG* 1.3 100.4 - - - +
1344A ALA* 1.3 62.9 + - - +
1346A GLN* 3.2 14.0 + - - +
1347A VAL* 3.3 12.5 + - - +
235B ASP* 5.3 0.7 - - - +
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Residues in contact with ALA1344 (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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1282A LEU* 5.4 1.0 - - - +
1297A LYS* 3.5 14.1 - - - +
1300A VAL* 4.3 12.5 - - + +
1301A VAL* 4.2 8.3 - - + -
1304A MET* 3.9 21.5 - - - -
1318A VAL* 4.4 13.0 - - + -
1329A ILE* 4.6 1.6 - - + -
1340A LEU 3.0 15.7 + - - +
1341A ARG 3.7 4.3 - - - +
1343A ILE* 1.3 78.1 - - - +
1345A SER* 1.3 62.1 + - - +
1347A VAL* 3.3 23.4 + - - +
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Residues in contact with SER1345 (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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1294A GLU* 4.3 3.3 - - - +
1297A LYS* 2.7 34.0 + - - -
1298A ALA* 6.4 0.4 - - - -
1301A VAL* 3.9 16.5 - - - +
1341A ARG 3.0 13.8 + - - -
1342A ARG* 2.6 24.9 + - - +
1344A ALA* 1.3 76.7 - - - +
1346A GLN* 1.3 57.0 + - - +
1347A VAL 3.4 1.1 - - - -
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Residues in contact with GLN1346 (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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1297A LYS* 3.9 2.2 - - - +
1328A TYR* 4.8 3.0 - - - -
1342A ARG* 2.7 57.4 + - - +
1343A ILE* 3.2 6.8 + - - +
1344A ALA 3.1 0.4 - - - -
1345A SER* 1.3 83.9 - - - +
1347A VAL* 1.3 64.6 + - - +
1348A LYS* 3.2 11.6 + - - +
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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