Contacts of the helix formed by residues 1334 - 1341 (chain A) in PDB entry 1FP7
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 VAL1334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1333A THR* 1.3 73.9 - - - +
1335A ARG* 1.3 65.6 + - - +
1337A LEU* 3.2 7.0 + - - +
1338A LYS* 3.2 38.3 + - - +
1356A LEU* 4.3 11.3 - - + +
1381A ILE* 4.6 1.8 - - + -
1382A ASN 4.8 1.5 + - - +
1387A ASP* 3.2 38.5 + - + +
1391A GLU* 4.0 24.0 - - + -
1392A LEU* 3.4 29.4 - - + +
1395A LEU* 4.3 14.8 - - + -
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Residues in contact with ARG1335 (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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1070A ALA* 4.9 17.2 + - - +
1333A THR* 3.4 4.0 + - - +
1334A VAL* 1.3 71.5 - - - +
1336A ALA* 1.3 59.8 + - - +
1337A LEU 2.8 10.5 + - - -
1338A LYS* 2.9 23.6 + - - +
1339A MET* 3.1 9.0 + - - +
1345A LYS* 4.1 14.8 + - - +
1348A LEU* 3.6 60.8 - - + +
1349A ALA* 4.7 5.3 - - - +
1384A PHE* 3.8 43.6 - - + -
1386A THR* 4.4 7.6 + - - +
1387A ASP* 3.9 14.3 + - - +
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Residues in contact with ALA1336 (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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1065A ILE* 4.6 8.6 - - + +
1066A THR 5.7 1.1 - - - +
1067A PRO* 6.4 0.2 - - + -
1068A THR* 3.7 19.4 - - + +
1070A ALA* 4.4 5.3 + - - +
1071A GLY 3.4 20.2 - - - +
1072A GLU* 5.3 3.1 - - + -
1333A THR* 2.9 22.2 + - - +
1335A ARG* 1.3 77.2 - - - +
1337A LEU* 1.3 59.0 + - - +
1338A LYS 3.5 0.2 - - - -
1339A MET* 3.9 8.9 - - - +
1340A HIS* 3.1 28.3 + - + -
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Residues in contact with LEU1337 (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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1065A ILE* 3.2 31.2 - - + -
1332A ALA* 4.5 3.1 - - + -
1333A THR 3.3 18.5 + - - +
1334A VAL 3.2 6.0 + - - +
1335A ARG 2.8 1.2 + - - -
1336A ALA* 1.3 76.4 - - - +
1338A LYS* 1.3 62.4 + - - +
1339A MET 3.1 1.8 - - - -
1340A HIS* 3.5 1.5 + - + +
1341A GLY 3.1 4.7 + - - -
1355A ALA 3.6 1.0 - - - +
1356A LEU* 4.3 9.4 - - + +
1359A GLY* 2.9 54.8 + - - +
1360A PHE* 4.1 5.2 - - - +
1362A ASN* 4.6 5.2 - - + -
1363A LEU* 4.2 21.3 - - + -
1395A LEU* 3.4 36.8 - - + -
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Residues in contact with LYS1338 (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 VAL* 3.2 26.8 + - - +
1335A ARG* 2.9 13.0 + - - +
1337A LEU* 1.3 75.3 - - - +
1339A MET* 1.3 62.0 + - - +
1341A GLY* 3.3 3.0 + - - -
1342A GLY 3.2 4.3 + - - -
1343A VAL* 3.0 33.1 + - + +
1348A LEU* 2.7 32.3 + - + +
1349A ALA* 4.4 3.0 + - - +
1350A THR 3.6 13.7 + - - +
1352A ASN* 4.1 19.5 - - + +
1355A ALA* 3.7 11.5 - - + +
1356A LEU* 3.5 28.9 - - + +
1387A ASP* 5.2 1.6 + - - +
1391A GLU* 3.1 32.3 + - - +
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Residues in contact with MET1339 (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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1068A THR* 3.9 18.6 - - + -
1069A PRO* 4.7 13.2 - - + -
1070A ALA* 3.5 28.5 - - + -
1335A ARG 3.1 6.0 + - - +
1336A ALA* 4.0 10.8 - - - +
1337A LEU 3.1 0.2 - - - -
1338A LYS* 1.3 74.6 - - - +
1340A HIS* 1.3 55.2 + - - +
1341A GLY 2.9 4.0 - - - -
1342A GLY* 2.6 27.4 + - - -
1343A VAL 3.6 15.6 - - - +
1344A PRO* 4.8 0.9 - - + -
1345A LYS* 4.5 18.8 - - + +
1348A LEU* 3.5 28.7 - - + -
1503A LEU* 4.0 29.8 - - + +
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Residues in contact with HIS1340 (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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1065A ILE* 4.9 1.1 - - + -
1066A THR* 2.8 48.3 + - + -
1068A THR* 3.8 14.2 - - + +
1336A ALA 3.1 22.0 - - - -
1337A LEU* 3.5 7.3 + - + +
1338A LYS 3.4 0.2 - - - -
1339A MET* 1.3 79.2 - - - +
1341A GLY* 1.3 60.3 + - - +
1342A GLY* 3.1 1.1 + - - -
1358A GLU* 4.3 3.1 - - - +
1359A GLY* 3.6 20.1 - - - +
1362A ASN* 3.4 24.7 + - + -
1494A TYR 4.9 0.4 - - - -
1503A LEU* 3.7 15.4 - - + +
1504A GLY* 2.7 47.4 + - - +
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Residues in contact with GLY1341 (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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1337A LEU 3.1 8.3 + - - -
1338A LYS 3.3 6.0 + - - -
1339A MET 2.9 1.6 - - - -
1340A HIS* 1.3 78.9 - - - +
1342A GLY* 1.3 55.0 + - - +
1343A VAL 3.7 1.1 - - - -
1355A ALA* 3.0 39.1 - - - +
1358A GLU* 3.9 10.2 - - - +
1359A GLY 3.4 7.0 - - - -
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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