Contacts of the strand formed by residues 150 - 158 (chain A) in PDB entry 2VOP
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 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A PHE* 3.6 23.6 - - + -
119A PRO 3.8 13.7 - - - -
120A THR* 3.0 51.6 - - - +
122A ALA* 3.8 22.0 - - + +
127A ILE* 3.9 9.4 - - + -
142A MET* 4.0 15.9 - - + -
143A ARG 3.3 14.1 - - - -
144A ARG* 3.4 21.2 - - - +
149A ALA* 1.3 68.5 - - - +
151A LYS* 1.3 53.9 + - - +
152A GLY* 2.6 29.9 + - - -
153A SER 3.4 22.7 - - - -
154A ILE* 3.7 16.4 - - + -
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Residues in contact with LYS 151 (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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116A LYS* 6.0 1.9 - - - +
120A THR* 4.9 4.4 + - - -
143A ARG* 2.9 33.0 + - + +
144A ARG 3.7 26.2 + - - +
145A THR* 3.7 31.9 - - + +
149A ALA 3.0 2.6 + - - -
150A PHE* 1.3 67.0 - - - +
152A GLY* 1.3 56.5 + - - +
153A SER* 3.2 14.3 + - - +
1193A SO4 3.3 34.6 + - - +
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Residues in contact with GLY 152 (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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116A LYS* 5.2 1.6 - - - -
117A GLY 3.4 8.5 + - - -
118A PHE* 2.9 54.7 + - - +
120A THR* 4.9 2.2 - - - -
150A PHE* 2.6 27.1 + - - -
151A LYS* 1.3 73.8 - - - +
153A SER* 1.3 57.6 + - - +
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Residues in contact with SER 153 (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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114A TYR* 3.9 22.4 - - - -
115A ILE 3.3 10.8 - - - -
116A LYS* 4.2 6.7 - - - +
143A ARG* 2.9 62.1 + - - +
150A PHE* 3.4 2.6 - - - -
151A LYS* 3.2 6.8 - - - +
152A GLY* 1.3 77.8 - - - +
154A ILE* 1.3 66.7 + - - +
1193A SO4 3.5 12.0 + - - -
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Residues in contact with ILE 154 (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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114A TYR* 3.5 4.2 - - - -
115A ILE* 3.0 40.7 + - + +
118A PHE* 4.2 17.0 - - + -
127A ILE* 3.7 34.5 - - + -
131A LEU* 5.1 0.7 - - + -
140A ILE* 4.4 3.8 - - + -
141A GLN 3.0 17.7 - - - +
142A MET* 4.0 3.8 - - + -
143A ARG* 3.8 2.5 - - - -
150A PHE* 3.7 22.9 - - + -
153A SER* 1.3 82.2 - - - +
155A PHE* 1.3 75.7 + - - +
156A VAL* 3.5 29.4 - - + -
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Residues in contact with PHE 155 (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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112A SER* 5.8 0.9 - - - -
113A VAL 3.3 8.7 - - - +
114A TYR* 3.5 28.3 - + + -
139A ASN* 3.8 3.3 + - - +
140A ILE* 3.6 2.3 - - - -
141A GLN* 2.7 70.1 + - + +
143A ARG* 3.7 33.9 - - + -
154A ILE* 1.3 78.9 - - - +
156A VAL* 1.3 63.8 + - - +
157A VAL* 4.3 2.4 + - + -
185A LYS* 3.8 46.2 - - + -
188A TYR* 4.1 17.3 - + - -
189A PHE* 4.7 4.9 - + - -
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ARG 3.6 1.2 - - - +
112A SER* 3.2 3.3 - - - -
113A VAL* 2.7 41.7 + - + +
115A ILE* 4.2 12.1 - - + -
131A LEU* 4.1 18.6 - - + -
137A VAL* 3.4 36.8 - - + -
139A ASN 3.5 2.5 - - - -
140A ILE* 4.7 4.5 - - + -
154A ILE* 3.5 31.0 - - + -
155A PHE* 1.3 75.2 - - - +
157A VAL* 1.3 64.9 + - - +
158A PHE* 4.0 20.8 - - + -
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A PHE* 4.1 24.7 - - + -
108A VAL* 4.7 13.0 - - + -
111A ARG* 3.4 15.3 - - + +
112A SER* 3.7 19.3 - - - +
137A VAL* 3.1 8.0 - - - +
138A LEU* 2.9 42.5 + - + -
139A ASN* 3.0 25.2 + - + +
155A PHE* 5.5 2.5 - - + +
156A VAL* 1.3 74.5 - - - +
158A PHE* 1.3 72.8 + - - +
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Residues in contact with PHE 158 (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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111A ARG* 2.9 50.8 + - - +
113A VAL* 3.4 30.1 - - + -
131A LEU* 5.5 2.7 - - + -
134A LYS* 4.0 20.6 - - + -
135A GLY* 4.4 8.5 - - - -
136A GLN 3.3 9.9 - - - +
137A VAL* 3.8 19.5 - - + -
138A LEU* 3.9 3.8 - - - -
156A VAL* 4.0 15.0 - - + -
157A VAL* 1.3 79.0 - - - +
159A ASP* 1.3 62.3 + - - +
160A SER 3.3 16.6 - - - +
163A SER* 4.1 12.8 - - - +
164A ALA* 3.8 14.4 - - + -
167A PHE* 3.6 31.6 - + + -
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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