Contacts of the strand formed by residues 112 - 118 (chain A) in PDB entry 4FOV
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A PHE* 4.4 0.4 - - + -
87A LEU* 4.2 13.0 - - + -
104A ILE* 4.5 1.6 - - + -
105A PHE* 3.4 14.1 - - - +
106A MET* 4.0 15.0 - - + -
110A GLY 3.7 1.2 + - - -
111A GLU* 1.3 75.1 - - - +
113A GLY* 1.3 62.4 + - - +
128A SER* 3.2 6.0 - - - -
129A ARG 2.9 30.7 + - - +
132A SER* 3.7 26.0 - - - +
133A LEU* 4.0 18.8 - - + -
146A LEU* 3.6 32.3 - - + -
159A MET* 4.2 11.2 - - + -
161A VAL* 4.0 7.4 - - + -
166A VAL* 3.9 18.6 - - + -
167A PHE* 5.0 0.9 - - + -
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Residues in contact with GLY 113 (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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104A ILE* 3.4 6.9 - - - +
105A PHE* 2.8 45.0 + - - +
112A ILE* 1.3 79.0 - - - +
114A VAL* 1.3 65.0 + - - +
127A PHE 3.1 13.7 - - - -
128A SER* 3.8 2.9 - - - -
159A MET* 4.5 1.3 - - - -
167A PHE* 4.3 6.3 - - - -
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Residues in contact with VAL 114 (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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102A PHE* 3.8 8.3 - - + -
103A SER 3.1 13.9 - - - +
104A ILE* 3.9 12.8 - - + -
105A PHE* 3.6 2.7 - - - -
113A GLY* 1.3 80.3 - - - +
115A GLU* 1.3 63.7 + - - +
116A ILE* 4.1 11.0 - - + -
126A LEU* 3.3 8.7 - - - +
127A PHE* 2.8 56.3 + - + +
148A PHE* 3.8 28.0 - - + -
159A MET* 3.7 22.7 - - + -
167A PHE* 4.3 3.1 - - + -
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Residues in contact with GLU 115 (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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101A TYR* 2.8 42.0 + - + -
102A PHE* 3.1 11.4 - - - -
103A SER* 3.0 39.1 + - - +
105A PHE* 4.1 9.7 - - + -
114A VAL* 1.3 76.7 - - - +
116A ILE* 1.3 63.6 + - - +
117A ARG* 3.7 18.4 + - + -
125A TYR 3.3 8.2 - - - +
126A LEU* 4.0 23.4 - - + +
199A TYR* 4.2 10.7 + - - -
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Residues in contact with ILE 116 (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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101A TYR 3.7 2.2 - - - -
102A PHE* 4.1 14.6 - - + +
114A VAL* 4.1 18.2 - - + -
115A GLU* 1.3 79.2 - - - +
117A ARG* 1.3 59.8 - - - +
123A ILE* 3.6 9.4 - - - +
125A TYR* 2.9 41.3 + - + -
127A PHE* 4.4 4.0 - - + -
148A PHE* 4.6 1.6 - - + -
157A TYR* 3.4 47.1 - - + -
175A LEU* 3.8 34.8 - - + +
177A ILE* 4.4 7.0 - - + -
180A ILE* 4.3 10.8 - - + -
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Residues in contact with ARG 117 (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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99A ASN* 3.1 51.1 + - - +
100A ASN* 3.3 2.4 - - - -
101A TYR* 2.9 73.0 + - - +
115A GLU* 3.7 17.4 + - + -
116A ILE* 1.3 86.7 - - - +
118A ASP* 1.3 60.5 + - - +
123A ILE 3.2 4.0 - - - -
124A ASN* 2.9 35.3 + - - +
125A TYR 4.7 1.6 - - - +
175A LEU* 4.2 2.2 - - - +
180A ILE* 3.4 11.3 - - - +
193A ARG* 4.0 4.9 - - - +
199A TYR* 5.1 1.4 + - - -
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Residues in contact with ASP 118 (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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99A ASN 4.2 0.2 - - - -
100A ASN* 3.6 10.1 + - - -
117A ARG* 1.3 75.0 - - - +
119A ALA* 1.3 58.7 + - - +
120A GLN* 3.1 13.9 + - - +
121A LYS* 2.6 52.5 + - + +
122A GLY 2.9 22.2 + - - -
123A ILE* 2.9 22.1 + - + -
124A ASN* 5.7 0.4 - - - -
175A LEU* 3.8 18.3 - - + +
180A ILE* 3.3 5.1 - - + -
181A ASN* 2.8 23.0 + - - +
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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