Contacts of the strand formed by residues 1486 - 1491 (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 ARG1486 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1343r ASP 4.0 20.4 - - - +
1344r ASP 5.4 1.1 - - - -
1345r ASN* 5.3 5.4 - - - +
1449r ASN 3.3 12.6 + - - +
1450r LEU* 4.8 5.8 - - + -
1451r PHE* 2.9 27.9 + - - +
1484r PRO* 4.0 3.8 + - - +
1485r ILE* 1.3 73.9 - - - +
1487r ILE* 1.3 59.5 + - - +
1488r VAL 4.2 0.2 - - - -
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Residues in contact with ILE1487 (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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1345r ASN* 3.2 32.0 - - + +
1346r VAL 3.5 3.1 + - - +
1451r PHE* 3.3 11.9 - - + +
1485r ILE 3.3 5.4 + - - +
1486r ARG* 1.3 75.4 - - - +
1488r VAL* 1.3 61.4 + - - +
1489r ALA* 6.2 1.1 - - + -
1504r LEU* 4.5 21.1 - - + +
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Residues in contact with VAL1488 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1346r VAL* 3.6 13.0 - - + +
1360r ALA* 5.8 5.6 - - + -
1363r ALA* 4.9 18.6 - - + -
1451r PHE 2.9 11.2 + - - +
1452r VAL* 3.2 12.1 - - + +
1453r VAL 2.9 23.6 + - - +
1486r ARG 4.2 0.2 - - - -
1487r ILE* 1.3 73.9 - - - +
1489r ALA* 1.3 62.0 + - - +
1490r LEU* 5.6 0.2 - - - +
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Residues in contact with ALA1489 (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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1346r VAL 3.1 10.8 + - - +
1347r PHE* 3.4 10.3 - - + +
1348r VAL* 3.0 25.3 + - - +
1453r VAL* 3.4 17.0 - - + +
1456r VAL* 4.7 10.3 - - + -
1487r ILE* 4.1 2.1 - - + -
1488r VAL* 1.3 75.0 - - - +
1490r LEU* 1.3 60.6 + - - +
1491r SER* 4.3 0.4 + - - -
1504r LEU* 5.2 14.4 - - + -
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Residues in contact with LEU1490 (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* 3.5 10.5 - - + +
1356r LYS* 4.5 21.5 - - + +
1360r ALA* 6.1 4.3 - - + -
1453r VAL 2.7 13.9 + - - +
1454r ASP* 4.1 11.9 - - + -
1455r GLU 2.7 29.5 + - - +
1456r VAL* 2.9 9.6 + - - -
1488r VAL 5.6 0.2 - - - +
1489r ALA* 1.3 75.7 - - - +
1491r SER* 1.3 58.8 + - - +
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Residues in contact with SER1491 (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 3.0 8.5 + - - +
1349r GLY* 3.1 6.7 - - - -
1350r ALA 3.1 23.2 + - - +
1356r LYS* 5.6 2.9 - - - +
1455r GLU* 4.5 3.1 - - - +
1456r VAL* 4.2 8.5 - - - +
1457r HIS* 4.0 21.5 - - - +
1489r ALA 4.3 0.2 - - - -
1490r LEU* 1.3 77.1 - - - +
1492r SER* 1.3 69.6 + - - +
1494r LEU* 5.0 7.6 - - - -
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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