Contacts of the strand formed by residues 134 - 139 (chain F) in PDB entry 5ANC
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 ILE 134 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F HIS* 3.4 31.2 - - + +
52F LEU 3.2 9.4 - - - +
53F ILE* 3.4 17.3 - - + -
89F VAL 4.4 2.7 - - - +
90F ARG* 3.3 45.4 - - + +
91F VAL* 3.9 2.1 - - - +
132F GLY 3.8 6.1 - - - +
133F GLN* 1.3 98.7 + - - +
135F ILE* 1.3 64.1 + - - +
136F PHE 3.2 28.9 - - - +
137F SER* 4.6 1.3 - - - -
166F VAL* 6.4 0.4 - - + -
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Residues in contact with ILE 135 (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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52F LEU* 2.8 36.1 + - + +
53F ILE* 3.7 3.4 - - - +
54F SER* 3.4 19.3 - - - +
60F LEU* 3.8 28.7 - - + -
89F VAL* 3.1 24.0 - - - +
91F VAL* 4.0 12.0 - - + +
129F VAL* 3.7 26.7 - - + -
133F GLN 3.9 2.5 - - - +
134F ILE* 1.3 79.0 - - - +
136F PHE* 1.3 77.8 + - - +
159F PHE* 4.7 4.5 - - + -
163F GLN* 3.3 27.8 - - - +
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Residues in contact with PHE 136 (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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51F HIS* 3.5 0.6 - - - -
52F LEU* 2.8 43.9 + - + +
65F ILE* 3.6 5.6 - - + -
68F GLY* 3.6 9.2 - - - -
69F ARG* 3.2 35.0 - - + -
72F CYS* 5.4 0.4 - - - -
87F MET* 3.3 44.6 - - + -
89F VAL* 3.3 30.1 - - + -
134F ILE* 3.2 9.1 - - - +
135F ILE* 1.3 84.6 - - - +
137F SER* 1.3 58.8 + - - +
152F LEU* 4.3 11.2 - - + -
155F SER* 4.9 3.6 - - - -
159F PHE* 3.4 39.0 - + - -
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Residues in contact with SER 137 (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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49F CYS* 4.4 2.9 - - - -
50F VAL 3.6 6.7 + - - -
51F HIS* 3.1 30.3 - - - -
87F MET* 3.3 25.1 - - - +
88F ARG 3.4 4.1 + - - -
89F VAL 3.9 5.7 + - - +
90F ARG* 3.8 23.0 + - - -
136F PHE* 1.3 74.4 - - - +
138F ILE* 1.3 66.8 + - - +
139F ARG 4.3 0.4 - - - -
173F PHE* 3.6 23.3 - - - -
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Residues in contact with ILE 138 (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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48F LEU 3.4 10.7 - - - +
49F CYS* 3.5 2.6 - - - +
50F VAL* 3.1 44.7 + - + +
72F CYS* 4.9 3.8 - - - -
85F PHE* 4.6 14.6 - - + -
86F HIS 3.1 20.2 - - - +
87F MET* 3.6 25.4 - - + -
137F SER* 1.3 82.3 + - - +
139F ARG* 1.3 67.0 + - - +
140F THR* 4.0 6.3 + - + +
148F VAL* 4.1 31.6 - - + +
151F ALA* 5.2 0.9 - - + -
152F LEU* 4.1 19.1 - - + -
173F PHE* 4.4 1.8 - - - -
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Residues in contact with ARG 139 (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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38F ARG 4.0 13.5 + - - -
39F LYS 4.8 2.0 + - - -
41F ALA* 2.8 31.8 + - - +
42F SER 3.7 10.4 + - - -
43F THR* 4.1 4.0 - - - +
46F PHE* 3.4 31.7 - - + +
48F LEU 3.4 5.2 - - - +
86F HIS* 2.8 60.3 + - + +
88F ARG* 5.8 0.8 - - - +
138F ILE* 1.3 73.3 - - - +
140F THR* 1.3 65.5 + - - +
171F TRP 3.9 14.1 - - - +
172F GLY* 3.8 22.0 + - - -
173F PHE* 3.6 28.7 - - + +
195F ALA* 3.5 33.7 + - - +
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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