Contacts of the helix formed by residues 132 - 140 (chain B) in PDB entry 3VYF
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 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B SER* 2.4 28.8 + - - -
131B GLY* 1.3 72.8 - - - -
133B ILE* 1.3 64.2 + - - +
134B GLU* 3.2 16.2 - - - +
135B GLN* 3.2 6.4 + - - +
142B PRO* 3.9 1.3 - - - -
195B LEU* 3.7 24.9 - - + -
198B THR* 3.7 9.0 - - - -
199B GLY* 3.3 37.6 + - - +
200B VAL* 3.4 13.7 - - - -
201B TRP* 3.5 31.9 - + - -
329B ARG* 3.0 54.1 - - - +
332B ASN* 3.7 16.4 - - - -
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Residues in contact with ILE 133 (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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132B PHE* 1.3 69.2 - - - +
134B GLU* 1.3 74.0 + - - +
135B GLN 2.9 5.8 - - - -
136B ALA* 2.7 36.2 + - + +
139B ARG* 3.4 56.9 + - - +
140B VAL 4.5 1.6 - - - +
141B THR* 4.3 17.3 - - + +
142B PRO* 3.6 31.7 - - + +
145B ASP* 4.3 11.3 + - - +
329B ARG* 6.0 0.2 - - - +
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Residues in contact with GLU 134 (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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132B PHE* 3.2 15.1 - - - +
133B ILE* 1.3 90.5 - - + +
135B GLN* 1.3 67.3 + - + +
136B ALA 3.4 2.0 - - - +
139B ARG* 5.8 6.3 - - - +
198B THR* 3.6 27.0 + - - +
199B GLY* 3.7 24.0 + - - +
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Residues in contact with GLN 135 (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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40B GLY 5.3 2.4 - - - +
41B SER* 5.2 2.2 - - - -
42B SER* 3.4 18.4 + - - +
43B ASN* 4.3 1.0 - - - +
131B GLY* 5.6 0.9 - - - -
132B PHE 3.2 4.8 + - - +
133B ILE 2.9 1.0 - - - -
134B GLU* 1.3 86.1 + - - +
136B ALA* 1.3 64.2 + - - +
137B ILE* 3.5 4.0 + - - +
199B GLY 3.1 26.4 + - - +
200B VAL* 4.8 13.7 - - + +
308B PRO* 6.0 4.2 - - - +
309B THR* 4.3 14.2 + - - -
402B VYF 4.1 46.9 - - + +
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Residues in contact with ALA 136 (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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42B SER* 3.7 22.9 - - - +
43B ASN* 3.8 3.6 - - - +
132B PHE 3.6 1.8 + - - -
133B ILE* 2.7 21.4 + - - +
134B GLU 4.8 1.9 - - - +
135B GLN* 1.3 78.3 - - - +
137B ILE* 1.3 61.9 + - - +
138B GLY 3.6 0.3 + - - -
139B ARG* 3.4 13.2 + - - +
140B VAL 3.4 32.3 - - - +
142B PRO* 4.6 0.2 - - + -
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Residues in contact with ILE 137 (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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43B ASN* 2.8 27.1 + - - -
79B LEU* 3.8 17.6 - - + +
80B THR 3.6 28.9 - - - +
81B LEU* 3.7 22.0 - - + -
82B ARG* 4.3 12.6 - - + +
135B GLN 3.5 1.8 + - - +
136B ALA* 1.3 69.2 - - - +
138B GLY* 1.3 64.8 + - - +
139B ARG 3.1 3.7 + - - -
140B VAL* 4.2 4.5 + - - +
402B VYF 3.3 34.5 - - + -
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Residues in contact with GLY 138 (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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79B LEU* 5.2 3.8 - - - -
92B LEU* 5.2 4.1 - - - +
136B ALA 3.6 0.4 + - - -
137B ILE* 1.3 77.3 - - - +
139B ARG* 1.3 70.7 + - - +
140B VAL* 3.0 15.3 + - - +
401B NAG 5.5 5.9 + - - -
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Residues in contact with ARG 139 (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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133B ILE* 3.4 48.3 + - + +
134B GLU* 5.7 5.1 - - - +
136B ALA* 3.4 17.5 + - - +
137B ILE 3.1 3.2 - - - -
138B GLY* 1.3 79.9 - - - +
140B VAL* 1.3 62.1 + - - +
141B THR* 3.5 3.3 + - - -
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Residues in contact with VAL 140 (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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42B SER 4.3 3.3 - - - +
43B ASN* 4.7 9.4 - - - +
79B LEU* 6.2 0.4 - - + -
92B LEU* 3.4 36.8 - - + -
106B GLN* 3.9 0.7 - - - +
107B MET* 3.2 44.0 - - + +
133B ILE* 4.8 0.7 - - - -
136B ALA* 3.4 20.1 - - - +
137B ILE 4.2 8.7 + - - +
138B GLY 3.7 11.4 - - - +
139B ARG* 1.3 75.8 - - - +
141B THR* 1.3 75.6 + - - +
142B PRO* 3.3 3.5 - - - +
401B NAG 5.8 4.5 - - - -
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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