Contacts of the helix formed by residues 141 - 149 (chain B) in PDB entry 3V3Q
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 ARG 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B GLY* 3.0 22.0 + - - +
131B LEU* 3.5 13.2 - - - +
140B HIS* 1.3 78.5 - - + +
142B LEU* 1.3 90.4 + - - +
144B CYS* 2.8 22.3 + - - +
145B ALA* 2.8 39.5 + - - +
149B GLY 5.7 1.2 + - - -
150B ASP* 5.9 0.6 - - - +
152B ILE* 3.8 10.1 - - + +
153B ASP* 3.0 37.4 + - - -
156B LEU* 3.6 28.5 - - + -
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Residues in contact with LEU 142 (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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58B GLU 3.5 20.2 - - - +
59B LEU* 6.3 0.9 - - + -
60B VAL* 3.8 27.9 - - + +
61B LEU* 4.5 24.6 - - + +
140B HIS* 3.1 23.0 - - + +
141B ARG* 1.3 110.7 - - - +
143B GLN* 1.3 62.0 + - - +
145B ALA* 4.0 13.2 + - + +
146B ARG* 5.1 7.1 + - - -
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Residues in contact with GLN 143 (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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55B LYS 2.7 27.2 + - - -
56B PHE* 3.6 4.3 - - - -
57B GLN* 3.0 48.3 + - - +
60B VAL* 3.9 12.6 - - + -
71B ASP* 5.1 6.9 - - - +
74B GLN* 3.9 14.7 - - - +
139B LEU* 3.6 16.9 - - + +
140B HIS 2.7 35.8 + - - +
142B LEU* 1.3 78.9 - - - +
144B CYS* 1.3 61.7 + - - +
145B ALA 3.4 0.4 + - - -
146B ARG* 4.9 3.2 + - - +
147B GLY 5.2 1.6 + - - -
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Residues in contact with CYS 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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74B GLN* 5.3 1.8 - - - -
78B LEU* 4.9 1.3 - - - -
131B LEU* 4.3 8.7 - - - -
133B PHE* 4.0 26.9 - - - -
139B LEU* 4.0 18.6 - - - -
140B HIS 3.8 10.3 - - - +
141B ARG* 2.8 9.2 + - - +
143B GLN* 1.3 82.7 - - - +
145B ALA* 1.3 58.0 + - - +
146B ARG 3.5 0.7 - - - -
147B GLY* 3.3 3.4 + - - -
148B PHE* 2.8 43.4 + - + +
152B ILE* 3.8 23.8 - - + -
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Residues in contact with ALA 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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141B ARG* 2.8 39.6 + - - +
142B LEU* 4.0 9.8 + - - +
143B GLN 3.4 2.4 - - - -
144B CYS* 1.3 76.2 - - - +
146B ARG* 1.3 59.1 + - + +
149B GLY* 2.6 39.3 + - - +
152B ILE* 4.3 9.4 - - + -
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Residues in contact with ARG 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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60B VAL* 5.3 10.3 - - - +
61B LEU* 6.2 2.6 - - - +
63B HIS* 4.3 14.1 - - - +
64B PHE* 2.9 38.9 + - + +
65B GLY* 3.3 21.3 + - - +
66B LYS 4.1 9.9 - - - +
67B GLU* 4.1 11.1 - - - +
68B ASP* 3.8 13.3 + - - +
71B ASP* 2.9 45.6 + - - +
142B LEU 5.1 7.8 + - - -
143B GLN 4.9 2.8 + - - +
145B ALA* 1.3 81.8 - - + +
147B GLY* 1.3 57.7 + - - +
149B GLY* 4.7 0.6 - - - -
241B ARG* 3.0 22.9 + - - -
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Residues in contact with GLY 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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71B ASP* 3.7 30.6 - - - +
72B VAL* 4.7 2.0 - - - -
75B PHE* 3.8 19.2 - - - +
143B GLN 5.2 1.8 + - - -
144B CYS 3.3 5.6 + - - -
145B ALA 3.2 0.4 - - - -
146B ARG* 1.3 80.8 - - - +
148B PHE* 1.3 58.4 + - - +
241B ARG* 2.9 23.3 + - - +
245B LEU* 4.4 4.0 - - - +
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Residues in contact with PHE 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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75B PHE* 3.7 29.8 - + - -
78B LEU* 3.8 35.4 - - + -
79B LEU* 5.2 0.9 - - + -
116B PHE* 4.2 22.9 - + - -
120B LEU* 5.1 0.9 - - + -
133B PHE* 4.2 14.1 - + - -
144B CYS* 2.8 40.3 + - + +
147B GLY* 1.3 75.1 - - - -
149B GLY* 1.3 61.3 + - - +
151B TRP* 3.3 36.1 + + + +
152B ILE* 3.6 33.7 - - + +
155B ILE* 4.4 4.5 - - + -
241B ARG* 3.2 18.2 - - - +
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Residues in contact with GLY 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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141B ARG* 5.7 0.8 + - - -
145B ALA* 2.6 25.9 + - - +
146B ARG 4.7 0.4 - - - -
147B GLY 3.3 3.0 + - - -
148B PHE* 1.3 71.5 - - - +
150B ASP* 1.3 67.0 + - - -
151B TRP 3.0 4.3 + - - -
152B ILE* 3.2 17.7 + - - +
241B ARG* 3.7 20.5 - - - +
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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