Contacts of the strand formed by residues 150 - 158 (chain B) in PDB entry 2VOO
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B PHE* 4.1 8.1 - - + -
119B PRO 3.5 17.9 - - - -
120B THR* 3.0 54.0 + - - +
122B ALA* 3.6 16.2 - - + +
127B ILE* 3.9 5.2 - - + -
142B MET* 3.7 39.9 - - + -
143B ARG 3.3 14.8 - - - -
144B ARG* 3.6 18.3 - - - +
145B THR* 5.2 0.2 - - - +
149B ALA* 1.3 74.6 - - - +
151B LYS* 1.3 61.5 + - - +
152B GLY* 3.6 23.3 - - - -
153B SER 3.4 21.1 - - - -
154B ILE* 3.8 15.9 - - + -
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Residues in contact with LYS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LYS* 5.6 4.7 - - - +
120B THR* 4.7 6.0 + - - -
143B ARG* 2.8 75.4 + - + +
144B ARG 3.5 24.9 + - - -
145B THR* 3.9 19.6 - - + +
149B ALA 3.3 0.8 + - - -
150B PHE* 1.3 73.4 - - - +
152B GLY* 1.3 59.4 + - - +
153B SER* 3.5 7.0 + - - +
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Residues in contact with GLY 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LYS* 5.2 2.0 - - - -
117B GLY 3.0 10.3 + - - -
118B PHE* 3.0 46.0 + - - +
119B PRO 4.7 1.6 - - - -
120B THR* 5.0 1.1 - - - -
150B PHE* 3.3 27.9 + - - -
151B LYS* 1.3 79.0 - - - +
153B SER* 1.3 59.0 + - - +
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B TYR* 3.8 21.5 - - - -
115B ILE 3.0 13.2 - - - -
116B LYS* 3.9 10.5 - - - -
118B PHE* 4.8 0.2 - - - -
143B ARG* 2.8 52.7 + - - +
150B PHE* 3.4 2.4 - - - -
151B LYS* 3.5 9.7 - - - +
152B GLY* 1.3 78.9 - - - +
154B ILE* 1.3 65.7 + - - +
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B VAL 3.7 0.2 - - - +
114B TYR* 3.5 5.7 - - - -
115B ILE* 2.7 44.7 + - + -
118B PHE* 3.6 28.3 - - + -
127B ILE* 3.7 31.9 - - + -
131B LEU* 4.8 0.9 - - + -
140B ILE* 4.3 4.0 - - + -
141B GLN 3.2 15.9 - - - +
142B MET* 3.9 6.3 - - + -
143B ARG* 4.2 3.4 - - - -
150B PHE* 3.8 23.1 - - + -
153B SER* 1.3 82.9 - - - +
155B PHE* 1.3 64.1 + - - +
156B VAL* 3.4 26.9 - - + -
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Residues in contact with PHE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B SER* 6.3 1.3 - - - -
113B VAL 3.2 9.2 - - - +
114B TYR* 3.6 29.2 - + + -
139B ASN* 3.7 3.0 + - - +
140B ILE* 3.5 0.7 - - - -
141B GLN* 2.8 70.7 + - + +
143B ARG* 3.7 32.5 - - + -
154B ILE* 1.3 72.3 - - - +
156B VAL* 1.3 64.9 + - - +
157B VAL* 5.7 1.6 - - + -
185B LYS* 3.9 48.7 - - + +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG 3.5 2.3 - - - +
112B SER* 3.0 3.5 - - - -
113B VAL* 2.7 42.5 + - + +
115B ILE* 4.1 12.1 - - + -
131B LEU* 4.0 14.4 - - + -
137B VAL* 3.5 37.9 - - + -
139B ASN 3.3 2.5 - - - -
140B ILE* 4.6 4.3 - - + -
154B ILE* 3.4 34.5 - - + -
155B PHE* 1.3 76.0 - - - +
157B VAL* 1.3 65.4 + - - +
158B PHE* 3.8 19.2 - - + -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PHE* 4.7 10.8 - - + -
108B VAL* 3.8 21.3 - - + +
111B ARG* 3.4 28.0 - - - +
112B SER* 3.4 19.3 - - - +
137B VAL* 3.0 5.9 - - - +
138B LEU* 2.8 39.3 + - + -
139B ASN* 2.9 35.9 + - + +
155B PHE* 5.7 2.0 - - + -
156B VAL* 1.3 76.7 - - - +
158B PHE* 1.3 58.8 + - - +
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG* 2.5 58.7 + - + +
113B VAL* 4.0 12.3 - - + -
131B LEU* 4.3 5.6 - - + -
134B LYS* 3.4 26.9 - - + -
135B GLY 4.4 1.8 - - - -
136B GLN 3.7 5.4 - - - -
137B VAL* 3.7 19.5 - - + +
138B LEU* 4.1 3.7 - - - +
156B VAL* 3.8 22.2 - - + -
157B VAL* 1.3 75.9 - - - +
159B ASP* 1.3 59.8 + - - +
160B SER 3.2 10.1 - - - +
163B SER* 3.4 25.4 - - - +
164B ALA* 4.0 10.5 - - + -
167B PHE* 3.7 42.8 - + + -
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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