Contacts of the helix formed by residues 1334 - 1345 (chain A) in PDB entry 3FK2
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 PRO1334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1330A ASP* 6.2 1.8 - - + -
1331A PRO* 4.1 9.2 - - + +
1332A LEU 3.1 6.9 - - - +
1333A VAL* 1.3 86.6 - - + +
1335A TYR* 1.3 66.0 + - - +
1336A ASN* 3.3 19.5 - - - +
1337A MET* 3.1 20.0 + - + +
1338A GLN* 3.0 17.3 + - - +
1364A PHE* 4.4 9.4 - - + -
1365A PRO* 4.1 21.8 - - + -
1368A ASN* 3.7 20.2 - - - +
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Residues in contact with TYR1335 (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 ASP* 5.7 3.1 - - + -
1331A PRO* 3.5 24.0 - - + -
1333A VAL 3.6 0.6 + - - -
1334A PRO* 1.3 72.7 - - - +
1336A ASN* 1.3 64.0 + - - +
1338A GLN* 3.0 35.5 + - + +
1339A ILE* 3.2 14.8 + - + +
1405A MET 3.3 10.5 - - - -
1406A ARG* 2.8 49.4 + - - +
1407A PRO* 4.7 2.9 - - + -
1408A ASP* 5.0 6.8 - - + +
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Residues in contact with ASN1336 (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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1334A PRO* 3.5 18.1 - - - +
1335A TYR* 1.3 73.9 + - - +
1337A MET* 1.3 90.0 + - + +
1339A ILE* 3.3 30.1 + - + +
1340A ASP* 3.6 10.9 + - - +
1365A PRO* 5.5 5.1 - - - +
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Residues in contact with MET1337 (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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1333A VAL* 4.6 1.1 - - + -
1334A PRO* 3.1 25.4 + - + +
1336A ASN* 1.3 99.2 - - + +
1338A GLN* 1.3 59.4 + - - +
1340A ASP* 3.2 21.1 + - - +
1341A LEU* 2.8 32.4 + - - +
1360A VAL* 3.7 7.0 - - + +
1363A LYS* 3.4 46.9 - - + +
1364A PHE* 3.7 37.5 - - + -
1365A PRO* 4.4 1.6 - - + -
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Residues in contact with GLN1338 (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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1331A PRO* 4.2 0.2 - - - +
1333A VAL* 3.0 30.4 + - + +
1334A PRO 3.0 12.4 + - - +
1335A TYR* 3.0 31.5 + - + +
1337A MET* 1.3 76.7 - - - +
1339A ILE* 1.3 55.9 + - + +
1341A LEU* 3.2 9.4 + - - +
1342A VAL* 2.8 35.6 + - - +
1405A MET* 2.6 46.8 + - + +
1407A PRO* 4.8 3.3 - - - +
1421A TYR* 3.6 30.8 + - + +
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Residues in contact with ILE1339 (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 TYR* 3.3 17.0 - - + +
1336A ASN* 3.5 17.9 - - + +
1337A MET 3.2 0.4 - - - -
1338A GLN* 1.3 77.4 - - + +
1340A ASP* 1.3 66.9 + - - +
1342A VAL* 3.2 6.8 + - - +
1343A GLU* 3.0 34.1 + - + +
1412B MET* 3.9 45.1 - - + +
1413B ASP 4.6 1.3 - - - +
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Residues in contact with ASP1340 (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 ASN 3.6 7.4 + - - +
1337A MET* 3.2 27.1 + - - +
1339A ILE* 1.3 77.4 - - - +
1341A LEU* 1.3 66.3 + - - +
1343A GLU* 3.1 10.1 + - - +
1344A ALA* 2.9 24.4 + - - +
1360A VAL* 3.4 24.3 - - + +
1363A LYS* 4.9 9.2 - - - +
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Residues in contact with LEU1341 (chain A).
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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1333A VAL* 3.8 17.5 - - + -
1337A MET 2.8 16.5 + - - +
1338A GLN* 3.4 9.9 - - - +
1340A ASP* 1.3 77.3 - - - +
1342A VAL* 1.3 63.0 + - - +
1344A ALA* 3.3 3.1 + - - +
1345A HIS* 3.1 22.5 + - - +
1357A LEU* 3.6 27.2 - - + +
1360A VAL* 3.7 24.9 - - + +
1361A LEU 5.2 0.2 - - - +
1364A PHE* 4.3 9.6 - - + -
1372A PHE* 6.1 0.4 - - + -
1405A MET* 3.6 29.8 - - + -
1421A TYR* 6.5 0.2 - - + -
1424A ILE* 3.8 14.3 - - + +
1428A PHE* 3.7 24.5 - - + -
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Residues in contact with VAL1342 (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 GLN 2.8 20.7 + - - +
1339A ILE* 3.2 6.0 + - - +
1341A LEU* 1.3 75.3 - - + +
1343A GLU* 1.3 67.9 + - - +
1345A HIS* 3.4 14.9 - - + +
1346A LYS* 3.6 12.7 + - + +
1420A THR* 4.0 21.5 - - + -
1421A TYR* 3.8 31.9 - - + +
1424A ILE* 4.0 8.7 - - + -
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Residues in contact with GLU1343 (chain A).
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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1339A ILE* 3.0 26.4 + - + +
1340A ASP* 3.1 12.5 + - - +
1342A VAL* 1.3 77.3 - - - +
1344A ALA* 1.3 67.0 + - - +
1346A LYS* 2.7 64.4 + - - +
1347A ILE* 4.2 2.3 + - - +
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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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1340A ASP 2.9 15.5 + - - +
1341A LEU 3.7 4.7 - - - +
1343A GLU* 1.3 74.5 - - - +
1345A HIS* 1.3 58.2 + - - +
1347A ILE* 2.9 35.6 + - - +
1353A LYS* 4.1 6.1 - - - +
1356A ALA* 3.3 42.1 - - + +
1357A LEU* 3.9 11.2 - - + +
1360A VAL* 4.7 2.9 - - + -
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Residues in contact with HIS1345 (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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1341A LEU 3.1 10.3 + - - +
1342A VAL* 3.4 12.1 - - + +
1343A GLU 3.1 0.2 - - - -
1344A ALA* 1.3 78.8 - - - +
1346A LYS* 1.3 59.8 + - + +
1347A ILE 3.2 0.4 - - - -
1348A ASN* 5.6 0.2 - - - +
1353A LYS* 2.9 62.9 + - - +
1357A LEU* 4.8 3.7 - - + +
1419A ARG 5.6 0.2 - - - -
1420A THR* 4.1 30.5 + - + -
1423A THR* 3.7 34.6 + - + +
1424A ILE* 4.2 18.5 - - + +
1427A LEU* 4.7 4.4 - - + +
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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