Contacts of the helix formed by residues 139 - 155 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A SER* 3.1 22.8 + - - -
136A PRO 3.8 1.7 - - - +
137A ALA 3.4 2.8 - - - -
138A LEU* 1.3 81.9 - - - +
140A PRO* 1.3 59.1 - - - +
141A GLU* 3.1 21.7 + - - +
142A ALA* 2.8 18.7 + - - +
143A ARG* 2.6 38.3 + - - +
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Residues in contact with PRO 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A SER* 1.3 87.2 - - - +
141A GLU* 1.3 72.5 + - - +
143A ARG* 3.7 13.6 - - + +
144A ALA* 3.1 25.1 + - - +
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER 5.0 0.4 - - - +
112A ALA* 3.3 19.1 - - - +
113A LEU 2.9 9.7 - - - +
114A ALA* 3.1 24.1 - - + -
115A PRO* 3.6 3.9 - - - +
139A SER* 3.1 22.1 + - - +
140A PRO* 1.3 92.0 - - - +
142A ALA* 1.3 59.7 + - - +
144A ALA* 5.0 1.1 - - - -
145A PHE 3.3 9.7 + - - -
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER 4.5 4.3 - - - +
113A LEU* 2.8 26.0 + - + +
135A THR* 3.2 26.4 - - + +
136A PRO* 4.0 1.1 - - - -
138A LEU* 4.4 6.3 - - + -
139A SER* 2.8 20.1 + - - +
141A GLU* 1.3 73.5 - - - +
143A ARG* 1.3 67.4 + - - +
144A ALA 3.2 1.8 - - - -
145A PHE* 3.2 4.4 + - - +
146A SER* 2.9 26.5 + - - -
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Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PRO* 3.3 26.6 + - - +
137A ALA* 4.9 2.4 + - - +
139A SER 2.6 17.2 + - - +
140A PRO* 3.7 13.1 - - + +
142A ALA* 1.3 72.2 - - - +
144A ALA* 1.3 62.7 + - - +
146A SER* 3.3 16.6 - - - -
147A LEU* 3.4 17.0 - - + +
171A TRP* 3.2 34.8 - - - +
175A GLU* 4.1 24.0 + - - +
179A PHE* 3.6 28.0 - - + +
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PRO* 3.6 20.8 - - + +
140A PRO 3.1 17.2 + - - +
141A GLU* 3.9 3.6 - - - +
143A ARG* 1.3 75.4 - - - +
145A PHE* 1.3 65.1 + - - +
147A LEU* 3.0 14.1 + - + +
148A TRP* 2.8 23.2 + - - +
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Residues in contact with PHE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA* 4.3 25.4 - - + -
53A VAL* 4.9 1.1 - - + -
113A LEU* 3.4 41.3 - - + +
114A ALA 3.3 21.8 - - - -
115A PRO* 3.6 11.1 - - - +
117A ALA* 3.4 22.2 - - + -
118A PHE* 3.7 19.5 - + - -
129A LEU* 6.5 0.2 - - + -
131A LEU* 4.6 8.1 - - + -
135A THR* 4.5 8.5 - - + -
141A GLU 3.3 3.2 + - - -
142A ALA 3.2 9.8 + - - +
144A ALA* 1.3 77.9 - - - +
146A SER* 1.3 58.5 + - - +
148A TRP* 3.2 23.2 + + - +
149A ALA* 2.6 53.4 + - + +
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.8 16.5 - - - +
135A THR* 4.1 6.9 - - - +
136A PRO* 3.4 23.8 - - - +
142A ALA 2.9 13.9 + - - -
143A ARG 3.3 8.1 - - - -
145A PHE* 1.3 85.5 - - - +
147A LEU* 1.3 65.0 + - - +
149A ALA* 3.1 13.7 - - - +
150A MET* 3.2 16.9 + - - +
179A PHE* 3.8 19.7 - - - -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ARG* 3.4 20.2 - - + +
144A ALA* 3.0 12.7 + - + +
146A SER* 1.3 76.3 - - - +
148A TRP* 1.3 63.4 + - - +
150A MET* 3.3 16.6 - - + +
151A GLU* 3.1 27.3 + - - +
179A PHE* 3.8 25.8 - - + -
182A ARG* 3.5 54.3 - - + +
183A ALA* 4.5 7.2 - - - -
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Residues in contact with TRP 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PRO* 3.9 18.6 - - + -
116A GLY* 3.2 36.0 - - - +
117A ALA 3.5 2.9 - - - -
118A PHE* 3.1 51.6 - + - -
120A PRO* 3.2 27.6 - - + +
144A ALA 2.8 14.9 + - - +
145A PHE* 3.4 25.1 - + - +
147A LEU* 1.3 73.2 - - - +
149A ALA* 1.3 75.3 + - - +
151A GLU* 3.2 16.1 + - - +
152A GLU* 2.9 46.1 + - + +
155A ARG* 5.9 0.2 - - - -
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A PHE* 4.9 4.9 - - + -
123A LEU* 3.9 2.8 - - - +
129A LEU* 3.3 15.5 - - + +
131A LEU* 4.1 11.9 - - + -
145A PHE* 2.6 47.7 + - + +
146A SER 3.1 7.2 - - - +
148A TRP* 1.3 84.6 - - - +
150A MET* 1.3 57.9 + - - +
152A GLU* 3.2 6.0 + - - +
153A ALA* 3.1 20.3 + - - +
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Residues in contact with MET 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 3.6 12.1 - - + +
131A LEU* 4.2 13.7 - - + -
146A SER 3.4 18.4 - - - +
147A LEU* 3.3 22.2 - - + +
149A ALA* 1.3 72.2 - - - +
151A GLU* 1.3 55.5 + - + +
152A GLU 3.1 2.0 - - - -
154A LYS* 2.7 35.3 + - - +
160A VAL* 3.4 38.4 - - + +
162A LEU* 5.2 7.6 - - + -
179A PHE* 4.5 7.6 - - + -
183A ALA* 4.1 38.8 - - + +
186A GLY* 4.4 12.7 - - - +
187A VAL* 4.7 4.7 - - + -
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Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.1 16.3 + - - +
148A TRP* 3.5 18.8 + - - +
150A MET* 1.3 78.5 - - - +
152A GLU* 1.3 58.1 + - - +
154A LYS* 3.9 9.0 - - - +
155A ARG* 3.1 48.8 + - - +
182A ARG* 5.8 1.4 + - - -
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Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A PHE* 5.7 0.4 - - + -
120A PRO* 3.2 41.8 - - + +
123A LEU* 3.9 5.5 - - + +
148A TRP* 2.9 36.3 + - + +
149A ALA* 3.3 7.9 - - - +
150A MET 3.1 0.2 - - - -
151A GLU* 1.3 76.7 - - - +
153A ALA* 1.3 61.8 + - - +
155A ARG* 2.9 39.0 + - - +
156A ARG* 3.1 44.8 + - - +
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.4 15.5 - - + +
129A LEU* 3.3 36.3 - - + -
149A ALA 3.1 3.8 + - - -
150A MET 3.3 2.9 + - - +
152A GLU* 1.3 73.8 - - - +
154A LYS* 1.3 60.2 + - - +
155A ARG 3.1 1.3 - - - -
156A ARG* 2.7 13.8 + - - +
157A GLY 3.0 0.2 + - - -
158A VAL* 2.7 46.1 + - + -
160A VAL* 4.2 5.2 - - + -
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Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A MET 2.7 19.0 + - - +
151A GLU* 3.9 7.9 - - - +
153A ALA* 1.3 75.5 - - - +
155A ARG* 1.3 60.1 + - - +
157A GLY* 3.0 18.9 + - - -
158A VAL 4.0 9.6 + - - +
160A VAL* 4.6 4.7 - - + +
185A PRO 4.2 15.6 + - - -
186A GLY* 5.0 15.2 - - - +
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Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TRP* 5.9 0.2 - - - -
151A GLU* 3.1 43.4 + - - +
152A GLU* 2.9 39.0 + - - +
153A ALA 3.1 0.4 - - - -
154A LYS* 1.3 76.8 - - - +
156A ARG* 1.3 70.7 + - - +
157A GLY 3.4 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