Contacts of the strand formed by residues 112 - 117 (chain F) in PDB entry 5IRC
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 112 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80F ILE* 3.5 8.5 - - + +
82F MET* 3.8 43.3 - - + -
100F THR* 5.2 1.6 - - + -
103F VAL* 3.9 29.2 - - + -
104F LYS* 4.1 28.7 - - + -
110F VAL 3.8 10.1 - - - +
111F PRO* 1.3 75.6 - - - +
113F ILE* 1.3 69.5 + - - +
114F LEU 4.2 2.0 - - - +
151F ILE* 4.6 13.9 - - + +
152F GLY 5.6 2.4 + - - +
153F ALA* 3.4 10.7 - - + +
154F PHE* 2.7 32.8 + - - +
155F GLY 3.8 0.2 + - - -
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Residues in contact with ILE 113 (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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79F VAL* 4.1 4.3 - - + -
80F ILE 2.8 14.9 + - - +
81F LEU* 3.7 21.7 - - + -
82F MET* 2.8 28.6 + - - -
112F ILE* 1.3 73.9 - - - +
114F LEU* 1.3 63.2 + - - +
115F VAL* 3.6 18.7 + - + +
154F PHE* 3.5 37.2 - - + -
155F GLY 3.8 4.9 - - - +
157F MET* 4.4 8.3 - - + -
170F VAL* 5.0 4.3 - - + +
173F MET* 3.7 31.0 - - + +
174F ALA* 4.0 13.7 - - - +
177F ALA* 4.2 9.2 - - + -
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Residues in contact with LEU 114 (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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82F MET* 3.3 23.8 - - - +
84F PHE* 4.0 17.0 - - + -
95F ILE* 3.8 32.3 - - + -
112F ILE* 3.8 2.6 + - - -
113F ILE* 1.3 71.9 - - - +
115F VAL* 1.3 60.6 + - - +
144F GLY 3.7 12.1 - - - +
147F MET* 4.0 15.9 - - + -
148F ALA* 3.5 35.0 - - + +
151F ILE* 4.4 4.9 - - + -
153F ALA* 4.3 7.2 - - + -
155F GLY 3.0 14.2 + - - +
156F TYR* 3.3 13.7 - - + -
157F MET 3.0 24.3 + - - -
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Residues in contact with VAL 115 (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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21F LEU* 4.0 8.7 - - + -
81F LEU* 4.2 8.3 - - + -
82F MET 2.8 9.6 + - - +
83F CYS* 3.3 16.2 - - - -
84F PHE* 3.0 32.2 + - - +
113F ILE* 3.8 27.1 - - + +
114F LEU* 1.3 76.7 - - - +
116F GLY* 1.3 61.1 + - - +
117F ASN* 3.3 24.4 + - - +
157F MET 3.3 8.1 - - - +
159F CYS* 3.8 17.3 - - - -
170F VAL* 4.1 20.6 - - + -
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Residues in contact with GLY 116 (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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84F PHE* 3.6 30.8 - - - -
86F ILE* 3.6 10.7 - - - +
114F LEU 4.2 0.4 + - - -
115F VAL* 1.3 70.4 - - - +
117F ASN* 1.3 62.7 + - - -
156F TYR* 4.2 4.5 - - - -
157F MET 2.8 12.8 + - - -
158F GLU* 3.3 3.5 - - - -
159F CYS 2.9 28.8 + - - +
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Residues in contact with ASN 117 (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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16F CYS 3.0 29.7 + - - +
17F GLY* 3.5 24.2 + - - -
18F LYS* 4.4 0.2 - - - +
21F LEU* 3.6 6.3 - - - +
83F CYS* 3.6 25.2 - - - +
84F PHE 2.7 12.8 + - - +
85F SER* 4.4 0.2 - - - -
86F ILE* 2.8 27.5 + - - +
115F VAL* 3.3 22.2 - - - +
116F GLY* 1.3 73.0 - - - -
118F LYS* 1.3 70.6 + - + +
119F LYS 3.3 2.4 + - - -
159F CYS* 3.3 15.4 - - - -
201F GDP 5.6 1.8 - - - +
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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