Contacts of the strand formed by residues 1172 - 1176 (chain E) in PDB entry 3F7P
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 HIS1172 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1159E VAL 3.5 0.5 - - - +
1160E LYS* 3.3 6.4 - - - -
1161E TYR* 2.7 78.4 + + + +
1162E TRP* 4.9 3.6 - - - -
1163E ILE* 6.0 4.5 - - + +
1170E GLU 3.8 13.9 + - - -
1171E ALA* 1.3 74.7 + - - +
1173E LEU* 1.3 64.2 + - - +
1192E TYR* 5.9 2.7 - + - -
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Residues in contact with LEU1173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158E ARG* 5.8 11.2 - - + -
1159E VAL 3.3 3.8 - - - +
1160E LYS* 3.6 41.5 - - + -
1171E ALA 4.7 5.2 - - - +
1172E HIS* 1.3 76.3 - - - +
1174E LEU* 1.3 67.2 + - - +
1207E TYR* 4.5 8.1 - - - +
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Residues in contact with LEU1174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158E ARG* 3.4 7.9 - - - +
1159E VAL* 2.8 50.2 + - + +
1161E TYR* 4.1 15.9 - - + +
1172E HIS 4.2 0.4 - - - -
1173E LEU* 1.3 77.7 - - - +
1175E ASP* 1.3 66.4 + - - +
1181E VAL* 3.6 28.5 - - + -
1182E GLU 3.9 10.5 - - - +
1183E LEU* 3.6 23.8 - - + -
1184E THR 5.5 0.7 - - - +
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Residues in contact with ASP1175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1157E TYR 3.4 10.0 - - - +
1158E ARG* 4.0 11.7 + - + +
1173E LEU 4.4 0.4 + - - -
1174E LEU* 1.3 85.2 - - - +
1176E SER* 1.3 66.7 + - - +
1177E LYS* 3.3 27.0 + - - +
1181E VAL* 4.6 5.2 - - - +
1199E TYR* 2.7 28.8 + - - -
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Residues in contact with SER1176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147E TRP* 4.8 7.9 - - - -
1156E GLY* 3.2 2.6 - - - -
1157E TYR 2.7 40.9 + - - -
1159E VAL* 5.5 1.6 - - - -
1175E ASP* 1.3 78.4 - - - +
1177E LYS* 1.3 65.9 + - - +
1178E VAL* 2.9 31.4 + - - +
1180E SER 2.9 17.0 + - - -
1181E VAL* 4.6 10.9 - - - +
1199E TYR* 4.1 1.4 + - - -
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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