Contacts of the helix formed by residues 129 - 141 (chain B) in PDB entry 3OVB
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 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B PRO* 4.0 17.7 - - + -
123B ILE* 3.6 30.2 - - + +
126B ALA 4.6 11.6 + - - +
127B VAL 3.1 1.8 + - - -
128B ASP* 1.3 77.5 - - - +
130B THR* 1.3 54.4 + - - +
131B PRO* 3.5 1.1 - - - -
132B PHE* 3.1 6.5 + - - +
133B HIS* 2.8 48.9 + - + +
218B ASP* 3.4 24.9 - - - -
220B VAL* 4.0 3.8 - - + -
221B ASP* 3.1 33.8 + - - +
224B ARG* 3.5 35.0 - - - +
31D C 4.7 10.3 + - - -
34D C 5.8 3.0 - - - +
35D A 5.8 1.8 - - - -
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Residues in contact with THR 130 (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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45B VAL* 3.8 14.5 - - + +
46B GLY 5.2 0.2 - - - +
50B ARG* 4.4 0.7 + - - -
63B PHE* 3.5 25.8 - - + -
127B VAL 3.2 12.7 + - - -
129B ARG* 1.3 79.0 - - - +
131B PRO* 1.4 65.4 - - - +
133B HIS* 3.2 25.2 + - - +
134B HIS* 3.2 9.0 + - - +
34D C 2.5 27.2 + - - -
35D A 3.5 29.7 + - - +
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Residues in contact with PRO 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.3 19.7 - - + -
45B VAL* 3.8 12.2 - - + +
63B PHE* 4.0 20.0 - - + -
65B LEU* 5.3 5.4 - - + -
114B CYS* 4.2 12.3 - - - -
115B TYR 6.0 0.2 - - - +
127B VAL 4.0 2.7 - - - +
128B ASP* 3.5 18.4 - - - +
130B THR* 1.4 94.9 - - - +
132B PHE* 1.3 64.0 + - + +
134B HIS* 3.4 4.0 + - - +
135B LYS* 3.2 33.9 + - + +
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Residues in contact with PHE 132 (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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115B TYR 5.6 0.4 - - - -
116B LYS* 6.2 0.7 - - - -
117B LEU* 3.2 39.7 - - + -
118B LYS* 4.9 0.7 - - - -
119B GLU 4.4 10.1 - - - -
120B PRO* 3.5 26.2 - - + -
128B ASP 3.5 23.3 - - - -
129B ARG 3.1 6.8 + - - +
131B PRO* 1.3 82.3 - - + +
133B HIS* 1.3 65.2 + - - +
134B HIS 3.1 1.6 - - - -
135B LYS* 3.3 12.2 + - + +
136B TRP* 3.2 23.7 + - - +
220B VAL* 3.7 25.3 - - + +
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Residues in contact with HIS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG* 3.8 3.4 - - - +
129B ARG* 2.8 41.2 + - + -
130B THR* 3.2 14.9 - - - +
132B PHE* 1.3 76.9 - - - +
134B HIS* 1.3 60.8 + - - +
136B TRP* 3.5 2.4 + - - +
137B LEU* 3.2 30.7 + - - +
173B TYR* 3.3 43.5 - + + -
218B ASP* 2.8 27.8 + - - -
220B VAL* 3.8 8.7 - - + -
35D A 3.0 46.0 + + - +
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Residues in contact with HIS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 5.8 1.6 - - + -
44B PHE 4.0 9.6 + - - -
45B VAL* 3.9 22.0 - - + -
46B GLY 3.9 4.2 + - - -
49B ALA* 3.3 47.2 + - + +
50B ARG* 3.4 33.0 + - + +
130B THR 3.2 3.6 + - - +
131B PRO 3.6 9.2 - - - +
132B PHE 3.1 0.4 - - - -
133B HIS* 1.3 79.2 - - - +
135B LYS* 1.3 72.1 + - - +
136B TRP 3.2 0.2 - - - -
137B LEU 3.8 0.5 - - - -
138B GLU* 2.9 44.5 + - + +
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Residues in contact with LYS 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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43B VAL* 4.5 23.0 - - - +
45B VAL* 6.6 0.2 - - - -
131B PRO* 3.2 20.9 + - - +
132B PHE* 3.3 16.3 + - + +
134B HIS* 1.3 83.8 - - + +
136B TRP* 1.3 61.1 + - - +
138B GLU* 3.2 43.1 + - - +
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Residues in contact with TRP 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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132B PHE 3.2 15.8 + - - +
133B HIS* 3.7 6.3 - - - +
135B LYS* 1.3 80.0 - - - +
137B LEU* 1.3 90.6 + - + +
138B GLU 3.6 0.2 + - - -
139B GLY 4.8 0.9 + - - -
140B ARG* 3.2 72.5 + - - +
173B TYR* 5.2 2.2 - - - +
177B LEU* 3.7 20.6 - - + -
180B VAL* 3.8 25.4 - - + -
203B VAL* 3.6 33.9 - - + -
204B ALA* 4.8 4.3 - - - +
219B PRO* 3.6 35.7 - - + +
220B VAL* 5.4 8.5 - - + -
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Residues in contact with LEU 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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50B ARG* 3.6 28.7 - - + +
133B HIS 3.2 14.3 + - - +
134B HIS 3.3 3.1 + - - +
136B TRP* 1.3 112.1 - - + +
138B GLU* 1.3 67.4 + - - +
139B GLY 3.4 0.4 - - - -
140B ARG* 4.0 4.9 - - - -
141B ILE* 3.1 34.7 + - + +
173B TYR* 3.8 21.5 - - + -
176B GLU* 3.4 45.8 - - + +
177B LEU* 4.1 4.5 - - + -
180B VAL* 5.0 3.6 - - + -
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Residues in contact with GLU 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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50B ARG* 5.7 1.8 - - - +
134B HIS* 2.9 39.2 + - + +
135B LYS* 3.2 47.1 + - - +
136B TRP 3.4 1.0 - - - -
137B LEU* 1.3 77.1 - - - +
139B GLY* 1.3 60.1 + - - +
141B ILE* 4.1 6.9 - - - +
142B LYS* 3.9 15.9 - - - +
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Residues in contact with GLY 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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136B TRP 4.8 1.0 + - - -
137B LEU 3.4 0.2 - - - -
138B GLU* 1.3 79.2 - - - +
140B ARG* 1.3 66.3 + - - +
141B ILE 3.1 2.7 - - - -
142B LYS* 3.1 35.5 + - - +
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TRP* 3.2 79.6 + - - +
137B LEU* 3.4 3.5 + - - +
139B GLY* 1.3 76.1 - - - +
141B ILE* 1.3 57.0 + - - +
142B LYS 4.5 2.0 - - - +
144B LYS* 3.9 17.5 - - - +
180B VAL* 4.2 25.8 - - + +
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Residues in contact with ILE 141 (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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50B ARG* 4.1 33.7 - - + +
52B THR* 4.1 11.7 - - + -
137B LEU* 3.1 28.2 + - + +
138B GLU 4.1 6.3 - - - +
140B ARG* 1.3 75.5 - - - +
142B LYS* 1.3 64.8 + - + +
144B LYS* 3.0 27.1 + - + +
145B GLU* 3.3 8.9 + - + +
148B VAL* 3.6 31.6 - - + -
176B GLU* 3.7 19.3 - - + +
179B ILE* 4.7 2.0 - - + -
180B VAL* 3.6 25.4 - - + -
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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