Contacts of the helix formed by residues 1329 - 1340 (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 ASN1329 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1327r PHE 3.9 1.2 + - - -
1328r PHE* 1.3 75.3 - - - +
1330r PRO* 1.3 62.1 - - - +
1331r ILE* 3.2 4.9 - - + +
1332r GLN* 2.9 10.2 + - + +
1333r THR* 2.8 25.4 + - - -
1354r SER 5.0 10.3 - - - +
1520r PRO* 4.4 25.1 - - + -
2202r ADP 4.0 14.8 + - + +
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Residues in contact with PRO1330 (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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1301r LEU* 5.8 7.0 - - + -
1302r LEU 5.2 10.4 - - - +
1304r LEU* 5.8 4.9 - - + +
1306r PRO* 6.2 2.6 - - + -
1328r PHE 4.0 0.4 - - - -
1329r ASN* 1.3 71.8 - - - +
1331r ILE* 1.3 62.4 + - - +
1333r THR* 4.3 6.6 - - - +
1334r GLN* 2.9 26.9 + - - +
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Residues in contact with ILE1331 (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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1329r ASN* 3.0 3.6 + - + +
1330r PRO* 1.3 76.7 - - - +
1332r GLN* 1.3 65.4 + - - +
1334r GLN* 3.0 6.8 + - - +
1335r VAL* 2.9 25.0 + - - +
1350r ALA* 5.1 8.3 - - + -
1354r SER* 4.3 25.6 - - - +
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Residues in contact with GLN1332 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1328r PHE* 3.9 17.7 - - + -
1329r ASN* 2.9 13.7 + - + +
1331r ILE* 1.3 80.7 - - - +
1333r THR* 1.3 56.9 - - - +
1335r VAL* 3.1 7.4 + - - +
1336r PHE* 2.8 31.7 + - - +
1354r SER 5.4 0.6 + - - -
1355r GLY 5.4 7.9 - - - +
1358r ILE* 6.3 2.2 - - + -
1359r CYS* 5.8 10.8 - - + +
2202r ADP 6.1 0.7 - - - +
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Residues in contact with THR1333 (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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1304r LEU* 5.1 10.6 - - - +
1305r GLN 4.6 6.1 - - - -
1306r PRO* 4.7 2.7 - - - -
1307r LEU* 3.7 37.2 - - - +
1328r PHE* 4.5 3.7 - - - +
1329r ASN 2.8 18.4 + - - -
1330r PRO* 4.3 6.5 - - - -
1332r GLN* 1.3 74.4 - - - +
1334r GLN* 1.3 60.9 + - - +
1336r PHE* 3.7 16.8 - - - +
1337r ASN 4.8 1.6 + - - -
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Residues in contact with GLN1334 (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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1301r LEU* 6.2 1.6 - - - -
1302r LEU* 5.4 17.3 - - + +
1304r LEU* 5.7 4.9 - - + +
1330r PRO 2.9 19.6 + - - +
1331r ILE* 3.0 4.9 + - - +
1333r THR* 1.3 79.6 - - - +
1335r VAL* 1.3 60.3 + - - +
1337r ASN* 4.9 2.4 + - - +
1338r THR* 5.3 3.3 + - - -
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Residues in contact with VAL1335 (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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1331r ILE 2.9 14.6 + - - +
1332r GLN* 3.7 6.5 - - - +
1334r GLN* 1.3 77.8 - - - +
1336r PHE* 1.3 66.5 + - - +
1337r ASN 3.5 0.4 - - - -
1338r THR* 3.0 11.3 + - - -
1339r VAL* 2.9 29.4 + - + +
1348r VAL* 5.5 10.1 - - + -
1359r CYS* 5.2 12.3 - - + -
1512r PHE* 5.6 6.7 - - + -
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Residues in contact with PHE1336 (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 2.8 16.8 + - - +
1333r THR* 3.7 14.4 - - - +
1334r GLN 3.3 1.8 - - - -
1335r VAL* 1.3 75.4 - - - +
1337r ASN* 1.3 57.5 + - - +
1339r VAL* 3.1 3.3 + - - -
1340r TYR* 2.7 42.2 + - + +
1362r PHE* 5.9 3.4 - - - -
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Residues in contact with ASN1337 (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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1333r THR 4.8 1.8 + - - -
1334r GLN 4.9 1.7 + - - +
1335r VAL 3.5 0.6 - - - -
1336r PHE* 1.3 78.3 - - - +
1338r THR* 1.3 63.1 + - - +
1340r TYR* 5.2 0.2 - - - -
1341r ASN* 3.2 31.0 + - + +
1342r SER* 3.3 9.5 + - - -
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Residues in contact with THR1338 (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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1334r GLN 5.3 2.4 + - - -
1335r VAL* 3.0 12.7 + - - -
1337r ASN* 1.3 79.9 - - - +
1339r VAL* 1.3 58.1 + - - +
1342r SER* 3.2 32.5 - - - +
1344r ASP 4.7 6.1 + - - +
1346r VAL* 5.6 6.7 - - - -
1509r THR 5.9 0.4 - - - -
1510r SER* 5.0 20.6 - - - -
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Residues in contact with VAL1339 (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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1335r VAL* 2.9 22.4 + - + +
1336r PHE* 4.1 1.8 - - - +
1338r THR* 1.3 77.8 - - - +
1340r TYR* 1.3 61.0 + - - +
1342r SER 3.6 8.0 - - - +
1344r ASP 5.7 1.8 - - - -
1346r VAL* 5.2 13.7 - - + -
1359r CYS* 4.4 18.2 - - + +
1362r PHE* 4.5 8.7 - - + -
1363r ALA* 3.9 23.0 - - + +
1366r ARG* 4.5 2.6 - - - +
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Residues in contact with TYR1340 (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* 2.7 23.9 + - + +
1337r ASN* 5.2 0.2 - - - -
1339r VAL* 1.3 73.8 - - - +
1341r ASN* 1.3 61.4 + - - +
1342r SER 3.1 6.8 + - - +
1362r PHE* 4.4 19.5 - - + +
1366r ARG* 3.7 24.9 - - + +
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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