Contacts of the helix formed by residues 1355 - 1371 (chain r) in PDB entry 6FF7
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 GLY1355 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1332r GLN* 5.4 7.3 - - - +
1353r GLY 3.5 1.4 + - - -
1354r SER* 1.3 74.5 - - - +
1356r LYS* 1.3 63.1 + - - +
1357r THR 3.1 4.4 + - - -
1358r ILE* 3.3 15.0 + - - +
1359r CYS* 3.7 5.5 + - - +
2202r ADP 2.5 52.6 + - - -
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Residues in contact with LYS1356 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1348r VAL* 5.1 11.7 - - + +
1350r ALA* 5.9 7.0 - - + +
1354r SER* 3.5 6.2 - - - -
1355r GLY* 1.3 74.3 - - - +
1357r THR* 1.3 64.6 + - - +
1358r ILE 3.2 0.2 - - - -
1359r CYS* 2.9 25.0 + - + +
1360r ALA* 2.9 12.6 + - - +
1490r LEU* 4.5 19.5 - - + -
1491r SER 5.6 3.4 - - - +
2202r ADP 3.4 14.0 + - - +
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Residues in contact with THR1357 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1355r GLY 3.1 0.8 - - - -
1356r LYS* 1.3 76.4 - - - +
1358r ILE* 1.3 58.0 + - - +
1360r ALA* 3.0 12.5 + - - +
1361r GLU* 2.9 22.7 + - - +
2202r ADP 3.2 28.1 + - - -
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Residues in contact with ILE1358 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332r GLN* 6.3 1.1 - - - -
1355r GLY 3.3 8.7 + - - +
1356r LYS 3.2 0.2 - - - -
1357r THR* 1.3 76.3 - - - +
1359r CYS* 1.3 61.4 + - - +
1361r GLU* 3.5 13.8 - - + +
1362r PHE* 2.9 26.7 + - - +
2202r ADP 5.3 11.4 - - + +
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Residues in contact with CYS1359 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332r GLN* 5.8 9.9 - - + +
1335r VAL* 5.2 14.6 - - + -
1339r VAL* 4.4 9.6 - - + +
1348r VAL* 5.2 11.0 - - + -
1355r GLY 3.7 3.5 + - - +
1356r LYS* 2.9 26.0 + - + +
1358r ILE* 1.3 79.0 - - - +
1360r ALA* 1.3 60.1 + - - +
1362r PHE* 3.2 20.5 - - - +
1363r ALA* 3.6 5.2 + - - +
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Residues in contact with ALA1360 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1356r LYS 2.9 10.3 + - - +
1357r THR* 3.0 12.1 + - - +
1359r CYS* 1.3 75.5 - - - +
1361r GLU* 1.3 63.0 + - - +
1363r ALA* 3.0 11.6 + - - +
1364r ILE* 3.0 21.3 + - - +
1452r VAL* 5.0 16.4 - - + -
1488r VAL* 5.8 5.8 - - + -
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Residues in contact with GLU1361 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1357r THR 2.9 6.8 + - - +
1358r ILE* 3.2 23.1 + - + +
1360r ALA* 1.3 78.8 - - - +
1362r PHE* 1.3 56.1 + - - +
1364r ILE* 3.5 9.9 - - - +
1365r LEU* 2.9 29.3 + - - +
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Residues in contact with PHE1362 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1336r PHE* 5.6 3.4 - - - +
1339r VAL* 4.5 12.1 - - + -
1340r TYR* 4.4 22.0 - - + +
1358r ILE 2.9 12.0 + - - +
1359r CYS* 3.2 14.6 - - - +
1361r GLU* 1.3 77.0 - - - +
1363r ALA* 1.3 58.4 + - - +
1365r LEU* 3.0 9.7 + - - +
1366r ARG* 2.9 26.3 + - - +
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Residues in contact with ALA1363 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1339r VAL* 3.9 21.1 + - + +
1359r CYS 3.6 4.6 + - - +
1360r ALA* 3.0 12.4 + - - +
1362r PHE* 1.3 79.4 - - - +
1364r ILE* 1.3 56.8 + - - +
1366r ARG* 3.3 4.6 + - - +
1367r MET* 3.0 28.2 + - - +
1488r VAL* 4.9 17.0 - - + -
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Residues in contact with ILE1364 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1360r ALA 3.0 13.3 + - - +
1361r GLU* 3.5 13.7 - - - +
1363r ALA* 1.3 76.5 - - - +
1365r LEU* 1.3 56.1 + - - +
1367r MET* 3.3 8.8 + - - +
1368r LEU* 2.9 26.2 + - - +
1376r CYS* 5.8 10.3 - - + -
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Residues in contact with LEU1365 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1317r PHE* 5.6 10.1 - - + -
1361r GLU 2.9 14.0 + - - +
1362r PHE* 3.0 10.1 + - - +
1364r ILE* 1.3 72.6 - - - +
1366r ARG* 1.3 66.0 + - - +
1368r LEU* 3.0 11.7 + - - +
1369r LEU* 2.9 20.8 + - - +
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Residues in contact with ARG1366 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1339r VAL 4.5 3.1 - - - +
1340r TYR* 3.7 24.7 - - - +
1342r SER 5.6 1.6 - - - +
1362r PHE 2.9 12.4 + - - +
1363r ALA* 3.5 12.1 - - - +
1365r LEU* 1.3 75.8 - - - +
1367r MET* 1.3 63.4 + - - +
1369r LEU* 3.0 10.7 + - - +
1370r GLN* 2.9 20.8 + - - +
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Residues in contact with MET1367 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1363r ALA 3.0 14.3 + - - +
1364r ILE* 3.5 11.0 - - - +
1366r ARG* 1.3 76.0 - - - +
1368r LEU* 1.3 62.3 + - - +
1370r GLN* 3.0 19.7 + - + +
1371r SER* 3.1 15.4 + - - +
1374r GLY* 4.9 9.1 - - - -
1375r ARG 5.7 0.4 - - - +
1376r CYS* 5.6 5.2 - - + -
1449r ASN* 4.9 12.8 - - + -
1450r LEU* 4.6 17.3 - - + -
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Residues in contact with LEU1368 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1364r ILE 2.9 15.0 + - - +
1365r LEU* 3.1 17.9 - - - +
1367r MET* 1.3 75.4 - - - +
1369r LEU* 1.3 61.5 + - - +
1371r SER 3.0 21.6 + - - +
1372r SER* 5.0 0.9 - - - -
1374r GLY* 6.4 0.2 - - - -
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Residues in contact with LEU1369 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1365r LEU 2.9 11.6 + - - +
1366r ARG* 3.0 10.3 + - - +
1368r LEU* 1.3 75.3 - - - +
1370r GLN* 1.3 64.6 + - - +
1371r SER* 3.4 0.9 + - - -
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Residues in contact with GLN1370 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1366r ARG 2.9 13.0 + - - +
1367r MET* 3.0 16.1 + - - +
1369r LEU* 1.3 78.7 - - - +
1371r SER* 1.3 62.8 + - - +
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Residues in contact with SER1371 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367r MET 3.1 8.0 + - - +
1368r LEU* 3.0 17.9 - - - +
1369r LEU 3.4 1.3 - - - -
1370r GLN* 1.3 81.2 - - - +
1372r SER* 1.3 67.6 + - - +
1373r GLU* 4.3 1.6 - - - -
1374r GLY* 3.4 25.0 + - - -
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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