Contacts of the strand formed by residues 1190 - 1194 (chain A) in PDB entry 1FNF
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 LEU1190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1178A THR* 3.4 6.4 - - - +
1179A THR* 2.8 40.7 + - - +
1188A ASN* 3.2 41.7 - - - +
1189A SER* 1.3 75.1 - - - +
1191A GLU* 1.3 65.7 + - - +
1203A PHE* 4.1 11.9 - - + -
1205A ASN* 3.0 42.6 - - - +
1206A LEU* 3.8 10.3 - - + -
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Residues in contact with GLU1191 (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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1176A ARG* 2.7 43.9 + - + +
1177A ILE 3.1 15.7 - - - +
1178A THR* 3.6 9.8 - - + +
1190A LEU* 1.3 79.5 - - - +
1192A GLU* 1.3 68.4 + - - +
1193A VAL* 4.4 6.4 - - - +
1203A PHE* 4.0 4.9 - - - -
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Residues in contact with GLU1192 (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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1176A ARG* 3.5 2.9 - - - +
1177A ILE* 2.8 32.0 + - + +
1191A GLU* 1.3 78.3 - - - +
1193A VAL* 1.3 85.8 + - - +
1194A VAL* 4.1 7.6 - - - +
1201A CYS* 3.8 28.1 - - + +
1202A THR 4.9 7.7 + - - +
1203A PHE* 3.8 20.4 - - + -
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Residues in contact with VAL1193 (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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1175A TYR 3.3 5.4 - - - +
1176A ARG* 3.5 30.5 - - + -
1191A GLU* 4.4 6.5 - - - +
1192A GLU* 1.3 95.9 + - - +
1194A VAL* 1.3 65.3 + - - +
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Residues in contact with VAL1194 (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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1164A TRP* 3.6 20.6 - - + -
1173A THR 4.5 0.7 - - - +
1174A GLY* 3.5 3.8 - - - -
1175A TYR* 2.9 51.0 + - + +
1177A ILE* 3.9 2.7 - - + -
1192A GLU* 4.1 6.5 - - - +
1193A VAL* 1.3 82.2 - - - +
1195A HIS* 1.3 71.4 + - - +
1198A GLN* 3.8 23.3 - - + +
1200A SER 3.9 10.5 - - - +
1201A CYS* 3.9 26.9 - - + -
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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