Contacts of the strand formed by residues 141 - 145 (chain F) in PDB entry 5JLH
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F TYR* 3.4 10.6 - - - +
138F SER* 2.8 36.0 + - - +
140F LEU* 1.3 82.1 - - - +
142F CYS* 1.3 59.8 + - - +
143F VAL* 4.3 10.8 - - + -
503F GLN* 4.2 1.3 - - - -
506F PHE* 3.2 45.1 - + - -
692F PHE* 3.9 12.3 - - + -
694F ARG* 3.1 60.8 - - + -
720F GLY 3.9 15.3 - - - -
721F VAL* 3.7 28.7 - - + -
724F GLY* 4.2 7.2 - - - -
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Residues in contact with CYS 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F TYR* 4.4 20.9 - - - -
136F THR 3.8 4.7 - - - -
137F TYR* 4.0 20.0 - - + -
141F PHE* 1.3 73.7 - - - +
143F VAL* 1.3 62.4 + - - +
144F VAL* 5.6 0.2 - - - -
173F HIS 4.1 13.9 - - - -
174F VAL* 4.9 2.0 - - - -
177F VAL* 3.7 25.6 - - + -
692F PHE 3.2 17.1 + - - +
693F VAL* 3.4 14.7 - - + +
694F ARG 2.8 25.9 + - - -
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Residues in contact with VAL 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F LEU* 4.3 26.2 - - + -
134F ILE 3.4 1.6 - - - +
135F TYR* 3.4 5.2 - - - -
136F THR* 2.6 50.1 + - - +
138F SER* 4.1 25.4 - - - -
141F PHE* 4.3 9.2 - - + -
142F CYS* 1.3 74.4 - - - +
144F VAL* 1.3 65.8 + - - +
145F ILE* 4.4 6.1 - - + -
694F ARG* 3.4 11.2 - - + -
696F ILE* 3.7 25.8 - - + -
716F LEU* 5.7 1.1 - - + -
721F VAL* 4.7 10.1 - - + -
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Residues in contact with VAL 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F ILE* 3.2 36.6 - - + -
135F TYR* 3.4 25.1 - - + -
142F CYS* 5.5 0.4 - - - -
143F VAL* 1.3 73.4 - - - +
145F ILE* 1.3 66.1 + - - +
146F ASN* 4.2 1.8 - - - +
207F ASN* 4.1 15.5 - - - +
693F VAL* 4.1 12.6 - - + -
694F ARG 2.8 17.7 + - - +
695F CYS* 3.7 24.0 - - + -
696F ILE* 3.0 25.1 + - - +
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Residues in contact with ILE 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F LEU* 4.3 37.9 - - + +
129F TYR* 4.0 27.0 - - + -
134F ILE* 3.1 25.7 + - - +
143F VAL* 4.4 8.1 - - + -
144F VAL* 1.3 80.8 - - - +
146F ASN* 1.3 65.2 + - - +
147F PRO* 3.1 10.4 - - - +
696F ILE* 3.4 31.0 - - + +
698F PRO* 3.7 24.0 - - + -
707F LEU* 4.5 15.9 - - + -
712F VAL* 5.5 2.2 - - + -
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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