Contacts of the helix formed by residues 139 - 155 (chain B) in PDB entry 1V1A
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 SER 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B SER* 3.2 29.6 + - - -
136B PRO 4.1 3.1 - - - +
138B LEU* 1.3 83.5 + - - +
140B PRO* 1.3 66.0 - - - +
141B GLU* 2.9 19.3 + - - -
142B ALA* 2.5 30.3 + - - +
143B ARG* 2.8 11.3 + - - +
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Residues in contact with PRO 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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139B SER* 1.3 83.4 - - - +
141B GLU* 1.3 75.6 + - - +
143B ARG* 3.2 9.8 + - + +
144B ALA* 2.9 23.0 + - - +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER 5.5 1.1 - - - -
112B ALA* 3.4 25.6 - - - +
113B LEU 3.1 6.4 - - - +
114B ALA* 3.6 18.6 - - + +
115B PRO* 4.8 0.2 - - - -
139B SER* 3.1 21.0 + - - -
140B PRO* 1.3 84.5 - - - +
142B ALA* 1.3 51.3 + - - +
144B ALA* 3.1 9.5 + - - +
145B PHE* 2.7 30.8 + - - +
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Residues in contact with ALA 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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111B SER 5.0 3.6 - - - +
112B ALA 4.8 0.2 + - - -
113B LEU* 3.3 15.4 + - + +
135B THR* 3.1 35.4 - - + +
136B PRO* 3.9 0.7 - - - -
138B LEU* 3.9 6.3 - - + -
139B SER* 2.5 30.0 + - - +
141B GLU* 1.3 75.0 - - - +
143B ARG* 1.3 58.5 + - - -
145B PHE* 2.9 5.0 + - - +
146B SER* 2.9 27.6 + - - -
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Residues in contact with ARG 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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136B PRO* 3.4 34.9 - - + +
139B SER 2.8 10.3 + - - +
140B PRO* 3.5 12.3 - - + +
142B ALA* 1.3 73.5 - - - +
144B ALA* 1.3 62.7 + - - +
146B SER* 3.5 8.8 + - - -
147B LEU* 3.6 23.4 + - + +
171B TRP* 4.6 7.8 - - - -
175B GLU* 4.2 28.9 + - - +
178B GLY* 4.3 5.3 - - - -
179B PHE* 4.0 38.1 - - + +
182B ARG* 6.1 1.0 - - - +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO* 3.4 27.3 - - + +
140B PRO 2.9 13.6 + - - +
141B GLU* 3.2 11.9 - - - +
143B ARG* 1.3 76.8 - - - +
145B PHE* 1.3 63.0 + - - +
147B LEU* 3.8 7.0 + - - +
148B TRP* 3.2 18.4 + - - +
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Residues in contact with PHE 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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7B ALA* 4.0 26.7 - - + -
53B VAL* 4.4 4.5 - - + -
113B LEU* 3.2 44.4 - - + +
114B ALA 3.5 18.4 - - - -
115B PRO* 3.7 7.4 - - - +
117B ALA* 3.2 24.9 - - + -
118B PHE* 4.0 13.9 - + - -
131B LEU* 5.2 3.4 - - + -
135B THR* 4.3 11.9 - - + -
141B GLU 2.7 5.4 + - - +
142B ALA 3.1 10.1 - - - +
144B ALA* 1.3 75.4 - - - +
146B SER* 1.3 71.0 + - - +
148B TRP* 3.3 23.9 + + - +
149B ALA* 2.8 31.5 + - + +
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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
----------------------------------------------------------
131B LEU* 3.8 16.3 - - - +
135B THR* 3.9 4.3 - - - +
136B PRO* 3.2 26.4 - - - +
142B ALA 2.9 15.4 + - - -
143B ARG 3.7 6.5 - - - -
144B ALA 3.4 0.4 - - - -
145B PHE* 1.3 80.5 - - - +
147B LEU* 1.3 66.3 + - - +
149B ALA* 3.0 15.9 + - - +
150B MET* 3.2 14.4 + - - +
179B PHE* 3.8 21.8 - - - -
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Residues in contact with LEU 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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143B ARG* 3.6 23.5 + - + +
144B ALA* 4.0 7.2 - - - +
145B PHE 3.4 0.2 - - - -
146B SER* 1.3 78.4 - - - +
148B TRP* 1.3 68.0 + - - +
150B MET* 3.0 24.5 - - + +
151B GLU* 3.2 9.6 + - - +
179B PHE* 4.2 13.7 - - + -
182B ARG* 3.6 50.5 - - + +
183B ALA* 3.5 31.6 - - + +
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Residues in contact with TRP 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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115B PRO* 3.6 18.4 - - + -
116B GLY* 3.0 40.6 - - - -
117B ALA 3.4 7.0 - - - -
118B PHE* 3.3 44.9 - + - -
120B PRO* 3.5 24.2 - - + -
144B ALA 3.2 17.4 + - - +
145B PHE* 3.6 13.5 - + - +
147B LEU* 1.3 78.4 - - - +
149B ALA* 1.3 74.2 - - - +
151B GLU* 3.2 15.4 + - - +
152B GLU* 3.0 45.9 + - + +
155B ARG* 5.4 0.9 - - - -
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PHE* 5.1 7.4 - - + -
123B LEU* 4.5 1.2 - - - +
129B LEU* 3.7 12.4 - - + +
131B LEU* 3.8 17.9 - - + -
145B PHE* 2.8 32.7 + - + +
146B SER* 3.0 12.5 + - - +
148B TRP* 1.3 79.7 - - + +
150B MET* 1.3 64.9 + - - +
152B GLU* 2.8 17.8 + - - +
153B ALA* 3.0 10.7 + - - +
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Residues in contact with MET 150 (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 LEU* 3.7 13.9 - - + +
131B LEU* 4.6 9.4 - - + +
146B SER* 3.2 35.7 - - - +
147B LEU* 3.0 26.0 - - + +
149B ALA* 1.3 76.0 - - - +
151B GLU* 1.3 52.4 + - - +
153B ALA* 2.9 2.1 + - - +
154B LYS* 2.7 37.3 + - - +
160B VAL* 3.5 34.7 - - + +
162B LEU* 6.2 2.7 - - + -
179B PHE* 4.3 4.0 - - + -
183B ALA* 3.6 39.9 - - + +
186B GLY* 5.3 7.2 - - - +
187B VAL* 4.7 3.4 - - - -
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Residues in contact with GLU 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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147B LEU 3.2 11.0 + - - +
148B TRP* 3.3 21.0 - - - +
149B ALA 3.0 0.8 + - - -
150B MET* 1.3 79.8 - - + +
152B GLU* 1.3 58.3 + - - +
154B LYS* 3.2 7.1 + - + +
155B ARG* 2.8 48.8 + - - +
182B ARG* 6.3 1.8 - - - +
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Residues in contact with GLU 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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118B PHE* 5.7 0.2 - - + -
120B PRO* 3.2 29.8 - - + +
123B LEU* 4.0 7.2 - - + +
148B TRP* 3.0 36.6 + - + +
149B ALA* 2.8 13.2 + - - +
151B GLU* 1.3 72.2 - - - +
153B ALA* 1.3 58.1 + - - +
155B ARG* 2.8 45.5 + - - +
156B ARG* 2.9 62.2 + - - +
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Residues in contact with ALA 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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123B LEU* 3.7 12.5 - - + +
129B LEU* 3.2 37.2 - - + -
149B ALA 3.0 2.8 + - - -
150B MET* 2.9 7.1 + - - +
152B GLU* 1.3 75.7 - - - +
154B LYS* 1.3 59.9 + - - +
155B ARG 3.1 1.1 - - - -
156B ARG* 2.8 19.3 + - - +
157B GLY 3.0 0.2 + - - -
158B VAL* 2.8 41.1 + - + +
160B VAL* 4.6 1.3 - - + -
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Residues in contact with LYS 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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150B MET 2.7 18.9 + - - +
151B GLU* 3.7 6.5 - - + +
153B ALA* 1.3 72.4 - - - +
155B ARG* 1.3 55.9 + - - +
157B GLY* 2.5 26.3 + - - +
158B VAL 3.8 11.6 + - - +
160B VAL* 5.1 5.6 - - + -
185B PRO 4.5 12.9 + - - -
186B GLY* 4.8 17.1 - - - +
188B ASP* 5.9 2.7 - - - +
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Residues in contact with ARG 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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148B TRP* 5.2 1.0 - - - +
151B GLU* 2.8 34.4 + - - +
152B GLU* 2.8 48.3 + - - +
154B LYS* 1.3 75.9 - - - +
156B ARG* 1.3 67.3 + - - +
157B GLY 3.3 0.7 + - - -
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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