Contacts of the helix formed by residues 143 - 149 (chain B) in PDB entry 1WVA
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 GLN 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B VAL* 4.2 2.5 - - - +
128B ASP 3.4 3.8 - - - -
130B ASN* 3.0 27.1 - - + +
131B THR 4.0 1.1 - - - -
132B PRO* 3.4 28.6 - - - +
135B THR* 3.2 34.4 + - - +
138B GLY 3.8 8.5 + - - -
139B ASN 3.5 14.7 + - - +
140B LEU* 3.2 30.0 + - + +
142B GLY* 1.3 84.9 - - - +
144B PRO* 1.4 69.0 - - - +
145B VAL 3.0 4.1 + - - -
146B SER* 2.8 23.2 + - - -
147B PHE* 3.5 13.5 - - + -
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Residues in contact with PRO 144 (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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101B HIS 3.6 22.7 - - - +
102B SER 4.2 0.4 - - - +
104B ALA* 4.1 9.0 - - + -
105B ILE* 3.4 31.8 - - + +
122B TRP* 3.8 16.8 - - + -
128B ASP* 3.8 8.1 - - + +
140B LEU 3.0 15.4 - - - +
141B HIS* 3.4 11.0 - - - +
142B GLY 3.7 0.9 - - - -
143B GLN* 1.4 88.8 - - - +
145B VAL* 1.3 63.5 + - - +
147B PHE* 3.3 13.7 + - - +
148B LEU* 3.5 18.7 + - + +
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Residues in contact with VAL 145 (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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122B TRP* 3.6 33.4 - - + -
127B THR 3.3 5.2 - - - +
128B ASP 3.0 17.8 + - - +
129B ILE* 3.8 17.7 - - + -
143B GLN 3.0 0.6 + - - -
144B PRO* 1.3 74.9 - - - +
146B SER* 1.3 59.3 + - - +
148B LEU* 3.4 8.9 + - + +
149B LEU* 3.3 32.0 + - + +
169B ILE* 5.4 2.9 - - + -
174B ILE* 4.2 13.9 - - + -
176B TYR* 3.1 30.1 - - + +
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Residues in contact with SER 146 (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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129B ILE* 3.6 14.3 - - - +
130B ASN 2.8 27.7 + - - -
131B THR* 3.7 11.7 - - - -
143B GLN 2.8 12.1 + - - -
145B VAL* 1.3 77.9 - - - +
147B PHE* 1.3 70.6 + - - +
148B LEU 3.5 0.3 + - - -
149B LEU 3.9 4.9 + - - +
152B LEU* 3.9 21.6 - - - +
156B ILE* 3.2 30.3 - - - +
167B PRO* 5.6 0.5 - - - +
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Residues in contact with PHE 147 (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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105B ILE* 4.3 24.5 - - + -
132B PRO* 3.7 24.7 - - + -
140B LEU* 4.4 13.5 - - + -
143B GLN* 3.5 32.3 - - + -
144B PRO 3.3 7.5 + - - +
146B SER* 1.3 90.8 + - - +
148B LEU* 1.3 58.9 + - - +
149B LEU 3.6 0.2 - - - -
156B ILE* 4.5 20.0 - - + -
157B PRO 5.2 0.2 - - - -
159B VAL* 4.1 13.0 - - + -
162B PHE* 3.8 41.5 - + + -
165B VAL* 3.4 26.6 - - + +
167B PRO* 3.7 14.5 - - - +
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Residues in contact with LEU 148 (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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104B ALA 4.7 0.9 - - - -
105B ILE* 3.6 38.1 - - + +
108B ILE* 3.6 37.0 - - + -
109B SER* 3.6 11.7 - - - +
122B TRP* 5.1 2.7 - - + -
144B PRO 3.5 20.4 - - - +
145B VAL* 3.4 10.0 + - + +
146B SER 3.3 0.4 - - - -
147B PHE* 1.3 81.3 - - - +
149B LEU* 1.3 59.2 + - - +
165B VAL* 5.4 2.2 - - + -
166B THR 5.5 0.7 - - - +
167B PRO* 3.2 5.6 - - - +
168B CYS* 2.9 41.2 + - - +
169B ILE* 3.1 26.3 + - + -
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Residues in contact with LEU 149 (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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129B ILE* 3.7 30.7 - - + -
145B VAL* 3.3 18.9 + - + +
146B SER 3.9 2.5 + - - +
147B PHE 3.6 0.6 - - - -
148B LEU* 1.3 75.2 - - - +
150B LYS* 1.3 64.5 + - - +
151B GLU* 3.9 6.7 - - - +
152B LEU* 3.1 31.1 + - + +
153B LYS 3.5 6.1 + - - -
167B PRO* 3.5 8.3 - - - +
169B ILE* 3.4 37.2 - - + +
170B SER 4.0 15.5 - - - +
171B ALA* 4.3 2.5 - - - +
174B ILE* 4.7 5.6 - - + -
193B LEU* 4.1 14.8 - - + -
195B ILE* 4.3 9.9 - - + -
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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