Contacts of the helix formed by residues 143 - 163 (chain B) in PDB entry 2VM6
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 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B ASP* 3.0 30.3 + - - +
142B MET* 1.3 82.3 - - - +
144B PRO* 1.3 67.9 - - - +
145B GLU* 3.2 20.2 + - - +
146B ILE* 3.1 40.4 + - + +
147B TRP* 3.3 11.3 + - - +
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Residues in contact with PRO 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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55A CYS* 3.9 23.8 - - - -
59A VAL* 4.0 22.4 - - + -
70A LEU* 4.5 11.0 - - + -
142B MET* 3.2 25.1 - - + +
143B ARG* 1.3 82.4 - - - +
145B GLU* 1.3 71.2 + - - +
146B ILE 3.2 0.2 + - - -
147B TRP* 3.2 1.3 + - + -
148B ILE* 2.9 38.0 + - + +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.3 3.8 - - + +
73A GLN* 3.4 55.0 - - + +
74A VAL* 3.8 15.1 - - - +
77A LYS* 3.9 13.7 + - + +
143B ARG* 3.2 26.9 + - - +
144B PRO* 1.3 95.4 - - - +
146B ILE* 1.3 59.4 + - - +
149B ALA* 3.0 31.7 + - - +
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Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 3.3 35.4 - - + -
143B ARG* 3.1 37.6 + - + +
145B GLU* 1.3 78.2 - - - +
147B TRP* 1.3 66.9 + - - +
149B ALA* 4.1 3.0 - - - +
150B GLN* 3.1 41.0 + - + +
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Residues in contact with TRP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASN 4.7 6.6 + - - -
52A LEU* 3.4 27.2 - - + +
54A SER* 3.9 17.9 - - - -
55A CYS* 3.4 52.5 - - + -
142B MET* 4.1 27.6 - - + -
143B ARG 3.3 7.6 + - - +
144B PRO 3.2 3.2 + - - +
146B ILE* 1.3 81.5 - - - +
148B ILE* 1.3 59.7 + - - +
150B GLN* 3.7 8.1 - - + +
151B GLU* 3.4 13.9 + - - +
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.8 21.8 - - + -
55A CYS* 3.9 12.3 - - - -
56A LEU* 4.1 19.7 - - + -
59A VAL* 4.8 1.1 - - + -
70A LEU* 4.3 10.1 - - + -
74A VAL* 3.7 25.8 - - + -
95A PHE* 3.6 34.3 - - + -
144B PRO* 2.9 40.4 + - + +
147B TRP* 1.3 68.0 - - - +
149B ALA* 1.3 66.4 + - - +
150B GLN 3.0 1.9 + - - -
151B GLU* 3.1 4.0 + - - +
152B LEU* 2.9 28.1 + - + +
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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
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74A VAL* 3.6 14.3 - - - +
77A LYS* 3.4 13.0 - - + +
78A GLU* 3.4 33.7 - - - +
145B GLU 3.0 23.8 + - - +
146B ILE* 4.1 2.2 - - - +
148B ILE* 1.3 76.4 - - - +
150B GLN* 1.3 56.4 + - - +
152B LEU* 3.8 2.4 - - - +
153B ARG* 2.9 33.6 + - - +
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Residues in contact with GLN 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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146B ILE* 3.1 31.1 + - + +
147B TRP* 3.7 8.7 - - - +
149B ALA* 1.3 80.4 - - - +
151B GLU* 1.3 62.1 + - - +
153B ARG* 3.7 7.7 - - - +
154B ARG* 3.1 23.3 + - + +
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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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48A VAL* 4.1 21.7 + - + +
51A ASN* 2.6 39.5 + - + +
52A LEU* 3.6 39.9 - - + +
147B TRP 3.4 2.3 + - - +
148B ILE 3.1 5.9 + - - +
150B GLN* 1.3 80.4 - - - +
152B LEU* 1.3 61.3 + - - +
154B ARG* 2.7 36.3 + - - +
155B ILE* 3.1 22.7 + - - +
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Residues in contact with LEU 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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48A VAL* 3.9 33.7 - - + -
74A VAL* 3.7 24.7 - - + -
75A MET* 3.9 3.6 - - + -
78A GLU* 3.4 30.7 - - - +
91A THR* 3.3 29.4 - - - +
94A ALA* 5.4 1.1 - - + -
95A PHE* 3.8 27.8 - - + +
148B ILE* 2.9 24.2 + - + +
149B ALA 3.8 1.6 - - - +
151B GLU* 1.3 76.2 - - - +
153B ARG* 1.3 54.4 + - - +
155B ILE* 4.0 3.8 - - - -
156B GLY* 2.8 30.3 + - - -
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Residues in contact with ARG 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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77A LYS 2.9 25.7 + - - -
78A GLU* 2.8 28.0 + - + +
80A GLU* 3.6 7.7 + - - +
81A ASP* 3.4 41.8 + - - +
88A ARG* 3.3 31.9 - - - +
149B ALA 2.9 17.7 + - - +
150B GLN* 3.7 7.6 - - - +
152B LEU* 1.3 78.0 - - - +
154B ARG* 1.3 61.5 - - - +
156B GLY* 4.0 0.2 - - - -
157B ASP* 3.1 33.4 + - - +
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 3.3 15.0 + - - -
51A ASN* 2.9 15.6 - - - +
150B GLN 3.1 17.7 + - - +
151B GLU* 2.7 44.1 + - - +
152B LEU 3.3 0.4 - - - -
153B ARG* 1.3 77.4 - - - +
155B ILE* 1.3 69.3 + - - +
157B ASP* 3.3 5.0 + - - +
158B GLU* 2.5 76.6 + - + +
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Residues in contact with ILE 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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44A VAL* 3.7 21.3 - - + +
47A GLU* 3.5 42.8 - - + +
48A VAL* 3.7 19.7 - - + -
91A THR* 3.8 12.1 - - + -
151B GLU* 3.1 17.2 + - - +
152B LEU* 3.5 5.6 - - - +
154B ARG* 1.3 88.6 - - - +
156B GLY* 1.3 68.5 + - - +
158B GLU* 3.7 9.4 - - - +
159B PHE* 3.0 49.6 + - + +
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Residues in contact with GLY 156 (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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87A GLY* 3.2 36.7 - - - -
88A ARG* 3.7 6.3 - - - -
91A THR* 3.6 5.6 - - - -
152B LEU 2.8 23.2 + - - -
153B ARG 4.0 0.9 - - - -
155B ILE* 1.3 74.3 - - - +
157B ASP* 1.3 56.8 + - - +
159B PHE* 4.8 1.1 - - - -
160B ASN* 2.9 24.1 + - - +
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Residues in contact with ASP 157 (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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83A ILE* 5.3 1.2 - - - +
85A ASN* 3.0 17.0 + - - +
88A ARG* 2.8 43.3 + - - +
153B ARG* 3.1 19.7 + - - +
154B ARG* 3.7 4.3 - - - +
156B GLY* 1.3 74.3 - - - +
158B GLU* 1.3 65.2 + - - +
160B ASN* 3.5 8.6 + - - +
161B ALA* 3.3 17.2 + - - +
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Residues in contact with GLU 158 (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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47A GLU* 4.1 7.8 - - - +
154B ARG* 2.5 55.1 + - + +
155B ILE* 3.7 11.8 - - - +
157B ASP* 1.3 71.8 - - - +
159B PHE* 1.3 61.5 + - + +
161B ALA* 2.8 22.0 + - - +
162B TYR* 3.0 50.0 + - + +
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Residues in contact with PHE 159 (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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40A VAL* 3.7 19.7 - - + -
43A SER* 3.9 24.2 - - - -
44A VAL* 3.6 32.5 - - + -
47A GLU* 4.2 12.3 - - - -
87A GLY* 4.7 7.9 - - - +
90A VAL* 6.1 0.4 - - + -
148A PHE* 4.1 7.3 - - + -
155B ILE* 3.0 45.1 + - + +
156B GLY* 4.0 3.1 - - - +
158B GLU* 1.3 75.7 - - + +
160B ASN* 1.3 63.5 + - - +
162B TYR* 3.1 32.8 + + - -
163B TYR* 3.3 36.6 + + - +
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Residues in contact with ASN 160 (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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85A ASN* 3.5 37.2 - - - +
86A TRP* 3.7 2.1 + - - -
87A GLY* 3.6 13.1 + - - +
147A LYS* 2.7 48.9 + - - +
1150A SO4 4.7 3.0 + - - -
156B GLY 2.9 19.5 + - - +
157B ASP 3.5 8.3 + - - +
158B GLU 3.2 0.2 - - - -
159B PHE* 1.3 78.3 - - - +
161B ALA* 1.3 56.2 + - - +
163B TYR 3.3 4.0 - - - +
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Residues in contact with ALA 161 (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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157B ASP 3.3 9.0 + - - +
158B GLU* 2.8 16.2 + - - +
160B ASN* 1.3 75.4 - - - +
162B TYR* 1.3 68.5 + - + +
163B TYR 3.4 3.4 + - - +
164B ALA* 5.5 2.9 - - - +
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Residues in contact with TYR 162 (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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158B GLU* 3.0 59.4 + - + +
159B PHE* 3.1 30.4 + + - +
161B ALA* 1.3 85.0 - - + +
163B TYR* 1.3 72.0 + + + +
164B ALA* 4.5 0.4 + - - -
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Residues in contact with TYR 163 (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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40A VAL* 4.2 12.8 - - + +
43A SER* 5.1 3.5 + - - -
147A LYS* 2.6 46.9 + - + +
148A PHE* 3.3 63.0 - + + -
149A GLU 5.3 2.2 - - - -
1150A SO4 4.2 0.2 + - - -
159B PHE* 3.3 37.0 + + - +
160B ASN 3.3 3.6 - - - +
161B ALA 4.4 1.8 - - - -
162B TYR* 1.3 90.5 - + + +
164B ALA* 1.3 57.4 + - - +
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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