Contacts of the strand formed by residues 1327 - 1332 (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 ALA1327 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A LEU 3.5 2.5 + - - +
1060A ILE* 3.6 12.8 - - + -
1061A LEU* 3.1 19.8 + - - +
1325A PRO* 3.6 3.9 - - - +
1326A ASP* 1.3 83.7 + - - +
1328A THR* 1.3 71.4 + - - +
1329A VAL* 6.3 0.7 - - + -
1375A VAL* 4.7 3.1 - - - +
1376A PRO* 3.4 20.6 - - + +
1378A VAL* 5.6 3.6 - - + -
1426A VAL* 5.0 7.0 - - + -
1429A THR* 4.4 8.1 - - - +
1430A LEU* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060A ILE* 5.1 0.2 - - - -
1061A LEU* 3.0 27.5 + - + +
1063A THR* 4.1 18.2 - - + -
1314A TYR* 3.2 25.9 + - - +
1325A PRO* 5.1 1.6 - - - +
1327A ALA* 1.3 85.4 + - - +
1329A VAL* 1.3 67.1 + - - +
1330A ILE 3.9 0.2 + - - -
1370A ILE* 4.1 23.6 - - + -
1375A VAL* 3.9 5.0 - - - +
1376A PRO 3.2 5.8 + - - -
1377A ALA* 3.2 4.2 - - - +
1378A VAL* 2.7 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060A ILE* 4.5 6.7 - - + +
1061A LEU 3.0 5.2 + - - +
1062A VAL* 3.3 15.9 - - + -
1063A THR 2.9 24.4 + - - -
1077A THR* 4.4 11.2 - - + -
1081A LEU* 4.3 15.0 - - + -
1327A ALA* 4.3 1.1 - - + -
1328A THR* 1.3 79.3 - - - +
1330A ILE* 1.3 63.4 + - - +
1378A VAL* 2.9 9.6 - - + +
1380A ALA* 3.8 26.0 - - + -
1422A LEU* 3.9 15.9 - - + -
1426A VAL* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A THR* 3.1 10.5 - - + +
1064A ALA* 4.0 13.7 - - - +
1065A ILE* 4.2 3.8 - - + -
1328A THR 5.0 0.4 - - - +
1329A VAL* 1.3 76.0 - - - +
1331A VAL* 1.3 65.5 + - - +
1363A LEU* 3.7 17.0 - - + -
1366A HIS* 3.5 32.5 - - + -
1367A ILE* 4.0 7.2 - - + -
1370A ILE* 3.7 21.8 - - + -
1377A ALA* 5.3 0.9 - - + -
1378A VAL 2.6 14.8 + - - +
1379A VAL* 3.2 33.8 - - + +
1380A ALA 2.6 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A VAL* 4.4 9.6 - - + -
1063A THR 2.8 14.8 + - - +
1064A ALA* 3.5 15.6 - - + +
1065A ILE* 3.2 27.5 + - - +
1072A GLU* 4.0 17.5 - - + +
1073A GLY 3.8 20.4 - - - +
1074A LYS* 4.6 5.2 - - - -
1077A THR* 3.8 33.9 - - + +
1329A VAL* 5.0 0.7 - - + -
1330A ILE* 1.3 74.8 - - - +
1332A ALA* 1.3 73.7 + - - +
1380A ALA* 4.0 10.5 - - + +
1382A ASN* 4.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065A ILE* 3.7 22.7 - - + -
1072A GLU* 5.8 0.9 - - - -
1330A ILE 4.1 0.4 + - - -
1331A VAL* 1.3 82.3 - - - +
1333A THR* 1.3 67.3 + - - +
1337A LEU* 4.5 4.0 - - + -
1363A LEU* 4.1 25.6 - - + -
1379A VAL* 4.7 8.5 - - + -
1380A ALA 3.9 3.4 + - - -
1381A ILE* 3.2 12.2 - - + -
1382A ASN 2.8 25.1 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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