Contacts of the strand formed by residues 1226 - 1229 (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 VAL1226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1165A THR* 3.6 11.3 + - - +
1166A TRP* 4.3 5.2 - - - +
1224A ARG 4.0 6.1 - - - +
1225A ILE* 1.3 78.6 - - - +
1227A VAL* 1.3 65.1 + - - +
1228A GLY 3.7 20.0 - - - +
1229A TYR* 4.2 24.0 - - + +
1235A PRO* 4.3 12.3 - - + -
1236A VAL 3.8 7.0 - - - +
1237A THR* 4.1 7.0 - - + +
1482A TYR* 3.8 22.7 - - + +
1518A LEU* 4.3 15.5 - - + +
1520A ALA* 4.1 10.8 - - + +
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Residues in contact with VAL1227 (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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1143A LEU* 4.0 25.1 - - + -
1147A VAL* 3.6 34.8 - - + -
1159A ILE* 5.4 3.1 - - + -
1164A ILE* 3.6 5.8 - - + +
1165A THR* 2.8 25.6 + - - -
1166A TRP* 3.0 26.5 + - + +
1225A ILE* 3.5 2.2 + - + +
1226A VAL* 1.3 74.6 - - - +
1228A GLY* 1.3 56.9 + - - +
1236A VAL* 3.0 33.3 + - + +
1237A THR 4.1 8.1 - - - -
1238A ALA* 4.4 8.5 - - - +
1241A LEU* 4.4 5.2 - - + -
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Residues in contact with GLY1228 (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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1159A ILE* 4.4 10.5 - - - -
1163A THR 3.7 14.4 - - - -
1164A ILE* 3.9 7.4 - - - +
1165A THR* 4.2 1.3 - - - -
1226A VAL* 3.7 5.2 - - - +
1227A VAL* 1.3 83.6 - - - +
1229A TYR* 1.3 71.6 + - - -
1236A VAL* 3.2 23.9 + - - +
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Residues in contact with TYR1229 (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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1159A ILE* 3.2 8.2 - - - +
1160A ASP 2.8 23.4 + - - -
1163A THR* 3.0 32.9 + - + +
1165A THR* 4.4 17.9 - - + -
1226A VAL* 4.2 17.5 - - + +
1228A GLY* 1.3 79.4 - - - -
1230A THR* 1.3 67.9 + - - +
1233A GLY* 2.7 31.0 - - - +
1234A LYS 3.4 9.2 - - - +
1235A PRO* 3.9 20.0 - - + -
1236A VAL* 4.3 1.8 - - - +
1476A ARG* 6.5 0.9 - - + -
1477A TYR* 4.0 23.4 + - - -
1480A LEU* 4.4 10.8 - - + +
1518A LEU* 4.8 5.9 - - - +
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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