Contacts of the strand formed by residues 1058 - 1064 (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 LYS1058 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057A GLY* 1.3 77.0 - - - +
1059A LEU* 1.3 60.9 + - - +
1060A ILE* 3.7 3.8 + - + +
1292A LEU* 4.6 1.8 - - - -
1296A ASP 3.1 8.6 + - - +
1297A TYR* 3.6 31.7 - - + -
1298A VAL 3.0 24.5 + - - +
1326A ASP* 3.0 35.8 + - + +
1430A LEU* 4.1 28.4 + - + -
1434A PRO* 6.1 3.6 - - - +
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Residues in contact with LEU1059 (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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1057A GLY 4.0 1.8 + - - -
1058A LYS* 1.3 70.4 - - - +
1060A ILE* 1.3 65.0 + - - +
1061A LEU 4.1 0.2 - - - -
1288A THR* 4.3 17.7 - - + -
1292A LEU* 4.4 16.8 - - + -
1298A VAL* 3.7 10.5 - - + +
1300A THR* 4.2 22.0 - - + -
1313A PHE* 4.3 13.7 - - + -
1323A PHE* 3.8 37.5 - - + -
1324A LYS 4.5 3.4 - - - +
1325A PRO* 3.8 29.4 - - + +
1326A ASP* 2.8 39.5 + - - +
1327A ALA 3.5 1.9 + - - -
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Residues in contact with ILE1060 (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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1058A LYS 4.0 9.0 - - - +
1059A LEU* 1.3 80.1 - - - +
1061A LEU* 1.3 66.3 + - - +
1062A VAL* 3.9 0.6 + - + -
1081A LEU* 4.2 20.6 - - + -
1085A LEU* 4.0 26.7 - - + -
1297A TYR* 4.5 15.5 - - + -
1298A VAL 3.0 15.3 + - - +
1299A VAL* 3.5 10.0 - - + +
1300A THR* 3.2 26.5 + - - +
1327A ALA* 3.6 12.3 - - + +
1329A VAL* 4.5 13.2 - - + -
1426A VAL* 4.4 21.3 - - + -
1430A LEU* 4.7 10.8 - - + -
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Residues in contact with LEU1061 (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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1059A LEU* 4.1 1.4 + - - +
1060A ILE* 1.3 74.0 - - - +
1062A VAL* 1.3 63.8 + - - +
1063A THR* 4.6 7.2 - - - -
1300A THR* 3.4 13.7 - - - +
1301A GLU 4.1 3.4 - - - -
1302A ALA* 3.9 17.9 - - + -
1310A ALA* 4.2 16.4 - - + -
1313A PHE* 3.6 58.3 - - + -
1314A TYR* 3.8 23.1 - - + +
1325A PRO* 5.4 2.8 - - + +
1327A ALA 3.1 7.7 + - - +
1328A THR* 3.0 42.8 - - + +
1329A VAL 3.0 2.8 + - - -
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Residues in contact with VAL1062 (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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1060A ILE* 5.6 0.2 - - + -
1061A LEU* 1.3 75.8 - - - +
1063A THR* 1.3 72.1 + - - +
1074A LYS* 4.0 12.6 - - + +
1077A THR* 4.7 6.1 - - + -
1078A SER* 3.8 24.7 - - - +
1081A LEU* 5.3 3.4 - - + -
1299A VAL* 3.8 20.9 - - + -
1300A THR 3.1 23.8 + - - +
1301A GLU* 3.4 19.7 - - - +
1302A ALA 3.5 7.1 + - - -
1329A VAL* 3.3 22.4 - - + +
1331A VAL* 4.4 12.3 - - + -
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Residues in contact with THR1063 (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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1061A LEU* 4.6 6.7 - - - -
1062A VAL* 1.3 75.6 - - - +
1064A ALA* 1.3 69.1 + - - +
1074A LYS* 4.2 11.0 - - - -
1302A ALA* 4.1 6.1 + - - -
1304A PHE 4.1 2.8 + - - -
1305A GLY 3.3 21.7 + - - -
1306A ALA* 3.5 24.2 - - + -
1310A ALA* 4.1 12.7 + - + +
1328A THR* 4.1 13.9 - - + -
1329A VAL 2.9 11.7 + - - +
1330A ILE* 3.1 11.2 - - + -
1331A VAL* 2.8 25.5 + - - +
1370A ILE* 4.3 3.8 - - + -
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Residues in contact with ALA1064 (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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1063A THR* 1.3 80.8 + - - +
1065A ILE* 1.3 70.2 + - + +
1067A PRO* 5.9 0.2 - - + -
1072A GLU* 5.1 12.3 - - + +
1074A LYS* 4.3 19.4 - - + +
1304A PHE 4.5 1.9 + - - +
1305A GLY* 3.4 1.3 - - - -
1306A ALA* 3.0 31.2 + - - +
1330A ILE* 4.0 6.3 - - - -
1331A VAL* 3.5 29.6 - - + +
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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