Contacts of the strand formed by residues 141 - 145 (chain A) in PDB entry 5I4E
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 PHE 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A TYR* 3.6 6.8 - - - -
138A SER* 2.5 58.4 + - - -
139A GLY 3.2 3.0 - - - +
140A LEU* 1.3 80.0 - - - +
142A CYS* 1.3 64.1 + - - +
143A VAL* 4.1 6.3 - - + -
167A ARG* 4.5 2.9 - - - -
506A PHE* 3.7 27.6 - + + -
510A MET* 3.7 28.9 - - + -
692A PHE* 3.7 27.8 - - + +
694A ARG* 3.6 28.3 - - + -
721A VAL* 3.5 29.8 - - + -
724A GLY* 3.9 8.7 - - - -
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Residues in contact with CYS 142 (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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135A TYR* 4.2 21.3 - - - -
136A THR 3.8 10.3 - - - -
137A TYR* 3.9 23.3 - - + -
141A PHE* 1.3 78.0 - - - +
143A VAL* 1.3 79.1 + - - +
173A HIS 5.0 1.1 - - - -
177A VAL* 4.0 24.5 - - + -
692A PHE 3.3 9.6 + - - +
693A VAL* 3.6 9.5 - - + -
694A ARG* 2.9 29.6 + - - +
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Residues in contact with VAL 143 (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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110A MET* 5.1 2.7 - - + -
125A LEU* 4.0 31.2 - - + -
134A ILE 3.7 0.7 - - - +
135A TYR* 3.4 3.6 - - - -
136A THR* 2.8 39.4 + - - +
138A SER* 3.8 20.0 - - - +
141A PHE* 4.1 9.6 - - + -
142A CYS* 1.3 81.2 - - - +
144A VAL* 1.4 65.2 + - - +
145A ILE* 4.9 2.2 - - + -
694A ARG* 3.6 7.2 - - + -
696A ILE* 3.9 23.8 - - + -
716A LEU* 4.8 1.6 - - + -
721A VAL* 4.2 22.2 - - + -
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Residues in contact with VAL 144 (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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134A ILE* 3.3 25.1 - - + +
135A TYR* 3.5 33.7 - - + -
143A VAL* 1.4 73.2 - - - +
145A ILE* 1.3 63.4 + - - +
146A ASN* 4.3 1.1 + - - -
202A ALA 5.8 0.2 - - - -
207A ASN* 3.7 22.7 - - - +
693A VAL* 3.5 30.3 - - + -
694A ARG 3.1 5.6 + - - +
695A CYS* 3.5 13.2 - - + +
696A ILE* 2.8 34.0 + - - +
1500A AOV 5.5 0.9 - - - +
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Residues in contact with ILE 145 (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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125A LEU* 4.1 33.2 - - + +
129A TYR* 3.2 49.1 - - + -
133A LEU 6.0 0.2 - - - +
134A ILE* 3.0 35.8 + - - +
143A VAL* 4.9 7.2 - - + -
144A VAL* 1.3 80.3 - - - +
146A ASN* 1.3 65.1 + - - +
147A PRO* 3.3 2.4 - - - +
696A ILE* 3.5 25.1 - - + +
698A PRO* 4.0 16.8 - - + -
707A LEU* 4.4 11.2 - - + -
712A VAL* 5.4 3.6 - - + -
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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