Contacts of the helix formed by residues 139 - 152 (chain A) in PDB entry 3V9G
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 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A MET* 2.9 41.7 + - + +
135A LEU* 4.1 3.1 - - + -
138A PRO* 1.3 87.4 - - + +
140A ARG* 1.3 66.2 + - - +
141A ALA 3.4 1.8 - - - -
142A GLU* 3.0 39.5 + - - +
143A ILE* 2.9 24.4 + - - +
244A ALA* 5.0 0.8 + - - +
247A ARG* 5.0 5.7 - - - +
248A ILE* 3.7 40.8 - - + +
251A GLU* 2.6 40.2 + - - -
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 2.5 39.4 + - - +
36A PRO 3.7 10.1 + - - -
38A LEU* 3.8 26.8 - - - +
40A PHE* 4.8 1.8 - - - -
46A GLU* 5.7 1.1 - - - -
135A LEU 3.1 20.3 + - - +
136A SER* 3.3 23.0 + - - +
137A GLY 3.1 15.1 + - - +
138A PRO 3.4 0.2 - - - -
139A ARG* 1.3 78.1 - - - +
141A ALA* 1.3 65.8 + - - +
143A ILE* 3.1 6.0 + - - +
144A LEU* 2.9 37.0 + - + +
159A GLU* 2.6 47.6 + - - -
163A ALA* 3.6 20.4 - - + +
164A ALA* 4.7 1.6 - - - +
167A ILE* 4.2 0.6 - - - +
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Residues in contact with ALA 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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46A GLU 5.2 0.7 - - - +
49A ALA* 3.6 43.3 - - + +
50A LEU* 3.8 9.9 - - + +
53A ALA* 3.6 6.2 - - + +
137A GLY 4.6 1.2 + - - -
138A PRO 4.8 3.0 + - - +
139A ARG 3.4 0.4 - - - -
140A ARG* 1.3 79.5 - - - +
142A GLU* 1.3 57.0 + - - +
144A LEU* 3.7 10.4 - - - +
145A ALA* 2.9 32.4 + - - +
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Residues in contact with GLU 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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53A ALA* 4.1 10.4 - - + +
138A PRO 5.2 2.8 + - - +
139A ARG* 3.0 51.1 + - - +
140A ARG 3.2 0.6 - - - -
141A ALA* 1.3 79.0 - - - +
143A ILE* 1.3 58.9 + - - +
145A ALA* 3.3 3.7 + - - +
146A LYS* 2.8 67.4 + - + +
244A ALA* 3.9 10.8 - - + +
248A ILE* 5.4 2.0 - - - -
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Residues in contact with ILE 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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135A LEU* 4.0 24.5 - - + +
139A ARG 2.9 13.6 + - - +
140A ARG* 3.4 11.9 - - - +
142A GLU* 1.3 75.6 - - + +
144A LEU* 1.3 66.7 + - + +
146A LYS* 3.6 4.4 + - - +
147A THR* 2.8 35.1 + - - +
162A ALA* 3.6 39.7 - - + +
163A ALA* 4.7 2.2 - - + +
213A THR* 3.6 21.5 - - + -
241A ALA* 4.3 7.2 - - + -
244A ALA* 4.5 13.2 - - + -
245A VAL* 4.1 12.6 - - + -
248A ILE* 4.8 4.3 - - + -
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Residues in contact with LEU 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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40A PHE* 3.4 35.9 - - + -
50A LEU* 3.9 13.5 - - + -
140A ARG* 2.9 28.5 + - + +
141A ALA* 3.7 8.1 - - - +
143A ILE* 1.3 78.4 - - + +
145A ALA* 1.3 58.6 + - - +
147A THR* 3.2 3.3 + - - -
148A MET* 2.9 35.6 + - - +
155A VAL 4.9 2.0 - - - +
158A ALA* 3.2 38.3 - - + +
159A GLU* 3.7 16.4 - - + +
162A ALA* 4.3 0.4 - - + -
163A ALA* 3.9 18.6 - - + +
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Residues in contact with ALA 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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50A LEU* 3.9 5.4 - - + +
53A ALA* 3.8 23.3 - - + +
54A LEU* 3.7 24.5 - - + +
57A LEU* 3.8 9.6 - - + -
141A ALA 2.9 19.2 + - - +
142A GLU* 3.3 4.9 + - - +
144A LEU* 1.3 77.8 - - - +
146A LYS* 1.3 55.8 + - - +
148A MET* 3.4 2.1 + - - +
149A VAL* 2.9 34.0 + - - +
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Residues in contact with LYS 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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57A LEU* 4.1 20.2 - - + -
62A GLU* 3.8 25.0 + - - -
142A GLU* 2.8 51.5 + - + +
143A ILE* 4.1 2.2 - - - +
145A ALA* 1.3 73.9 - - - +
147A THR* 1.3 60.0 + - - +
149A VAL 4.6 0.2 - - - +
150A GLY* 2.9 25.6 + - - -
151A GLN* 4.0 3.3 - - - +
240A LEU* 3.7 35.9 + - + +
241A ALA* 4.0 15.8 + - + +
243A TYR* 6.2 0.2 - - - -
244A ALA* 3.6 27.3 - - + +
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Residues in contact with THR 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 ILE 2.8 22.8 + - - -
144A LEU 3.6 3.8 - - - -
146A LYS* 1.3 75.8 - - - +
148A MET* 1.3 65.0 + - - +
151A GLN* 3.0 35.8 + - - +
152A GLY 3.5 1.7 + - - -
153A LYS* 3.5 31.4 + - + -
158A ALA* 4.2 7.2 - - + -
161A ASP* 4.0 4.0 - - - +
162A ALA* 3.3 13.8 - - + +
213A THR* 3.2 27.0 + - - +
241A ALA* 3.6 5.2 - - - +
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Residues in contact with MET 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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50A LEU* 4.0 26.7 - - - -
54A LEU* 4.2 19.1 - - + -
85A PHE* 3.5 8.8 - - - -
144A LEU* 2.9 21.9 + - - +
145A ALA* 3.7 3.6 - - - +
147A THR* 1.3 76.1 - - - +
149A VAL* 1.3 58.6 + - + +
152A GLY* 3.0 27.9 + - - -
153A LYS 3.3 21.3 + - - +
154A THR 4.2 0.7 - - - +
155A VAL* 3.8 34.8 - - + +
158A ALA* 3.7 13.9 - - + -
380A PRO* 3.5 30.5 - - + +
381A ALA* 4.3 1.8 - - + +
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.9 20.0 - - + +
57A LEU* 4.0 24.0 - - + -
83A SER* 3.1 28.2 + - - +
84A PRO* 3.6 2.6 - - - +
85A PHE* 4.2 13.5 - - + -
89A HIS* 4.8 8.1 - - + +
91A VAL* 3.5 27.4 - - + -
145A ALA 2.9 18.3 + - - +
146A LYS* 4.5 0.9 - - - +
148A MET* 1.3 78.3 - - - +
150A GLY* 1.3 62.1 + - - +
240A LEU* 4.7 2.9 - - + -
381A ALA* 4.9 5.8 - - + -
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Residues in contact with GLY 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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81A GLN* 3.0 31.7 + - - +
82A VAL 4.0 4.0 - - - +
83A SER* 5.1 0.2 - - - -
84A PRO* 3.5 13.7 - - - +
91A VAL* 4.3 10.5 - - - -
146A LYS 2.9 17.5 + - - -
149A VAL* 1.3 81.8 - - - +
151A GLN* 1.3 58.7 + - - +
237A THR* 3.3 6.1 - - - +
240A LEU* 4.8 2.0 - - - -
392A ILE* 4.3 0.7 - - - +
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Residues in contact with GLN 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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81A GLN* 5.2 0.2 + - - -
84A PRO* 3.5 8.4 - - - +
146A LYS 4.0 1.6 - - - +
147A THR* 3.0 37.5 + - + +
150A GLY* 1.3 74.9 - - - +
152A GLY* 1.3 59.9 + - - +
153A LYS* 3.5 3.1 - - + +
161A ASP* 4.8 0.4 + - - -
210A PHE 3.1 26.1 + - - +
211A ASN 4.7 2.8 + - - -
212A PHE* 4.7 0.2 - - - +
213A THR* 3.1 26.8 + - - +
237A THR 3.5 18.6 - - - +
238A ALA* 3.6 17.5 - - + +
241A ALA* 3.5 16.1 + - - +
343A TYR* 3.1 28.4 + - + +
390A ALA 4.9 1.7 - - - +
392A ILE* 3.5 17.5 - - + +
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Residues in contact with GLY 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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84A PRO* 3.8 12.9 - - - +
85A PHE* 4.1 13.9 - - - -
147A THR 3.5 0.2 + - - -
148A MET 3.0 14.5 + - - -
150A GLY 3.8 1.0 - - - -
151A GLN* 1.3 79.4 - - - +
153A LYS* 1.3 64.1 - - - +
154A THR 3.9 0.7 + - - -
343A TYR* 4.0 10.4 - - - -
380A PRO* 4.6 1.6 - - - -
389A SER* 3.5 25.6 + - - -
390A ALA 4.6 4.0 - - - +
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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
------------------------------------------------------------
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