Contacts of the helix formed by residues 131 - 148 (chain B) in PDB entry 6VSU
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 ASP 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B GLY 3.5 3.9 + - - +
130B VAL* 1.3 78.5 - - - +
132B ASP* 1.3 58.8 + - - +
133B ASP* 3.0 13.9 + - - +
134B ARG* 2.9 45.7 + - - +
135B LEU* 3.0 21.4 + - - +
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Residues in contact with ASP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B HIS* 2.8 35.7 + - - -
75B ASN* 4.2 12.7 + - - +
126B ARG* 5.9 0.2 - - - +
130B VAL 5.3 0.9 - - - +
131B ASP* 1.3 72.1 - - - +
133B ASP* 1.3 65.6 + - - +
135B LEU* 3.8 9.9 - - - +
136B MET* 2.9 29.6 + - + +
197B ASN* 4.8 5.4 - - - +
199B TYR* 3.6 25.3 - - + -
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASP* 3.0 12.0 + - - +
132B ASP* 1.3 78.2 - - - +
134B ARG* 1.3 59.8 + - + +
136B MET* 3.3 2.4 + - - +
137B ASN* 3.0 38.8 + - - +
198B LYS* 3.1 23.1 + - - -
199B TYR* 2.6 34.5 + - - +
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Residues in contact with ARG 134 (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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30B GLU* 3.5 31.8 + - - +
33B GLN* 2.6 45.4 + - - +
34B ASN* 3.1 27.1 + - - -
37B ILE* 4.0 14.1 - - + +
129B GLY 5.2 0.4 + - - -
130B VAL* 3.8 23.1 - - + +
131B ASP* 2.9 28.0 + - - +
133B ASP* 1.3 76.0 - - + +
135B LEU* 1.3 66.3 + - - +
137B ASN* 3.3 14.0 + - - +
138B VAL* 3.1 25.6 + - - +
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Residues in contact with LEU 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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72B LEU* 3.9 15.9 - - + -
74B HIS* 3.6 30.7 - - + -
120B VAL* 5.6 0.2 - - + -
122B VAL* 4.3 23.1 - - + +
125B ILE* 4.2 26.0 - - + -
126B ARG* 3.9 16.6 - - + -
130B VAL* 3.8 11.6 - - + +
131B ASP 3.0 20.0 + - - +
132B ASP* 3.8 11.9 - - - +
133B ASP 3.3 0.2 - - - -
134B ARG* 1.3 76.9 - - - +
136B MET* 1.3 65.0 + - - +
138B VAL* 3.1 15.9 + - + +
139B ILE* 3.2 15.1 + - + +
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Residues in contact with MET 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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72B LEU* 4.3 10.3 - - + -
75B ASN* 3.8 12.6 - - - +
132B ASP* 2.9 23.5 + - - +
133B ASP 3.8 3.8 - - - +
135B LEU* 1.3 77.4 - - - +
137B ASN* 1.3 61.1 - - - +
139B ILE* 3.3 20.3 + - - -
140B SER* 3.1 18.9 + - - -
162B SER* 3.4 46.7 - - - +
163B ILE* 4.3 1.8 - - - +
166B PRO* 3.2 30.6 - - + +
169B ARG* 3.6 8.5 - - - +
199B TYR* 3.5 35.9 - - + +
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Residues in contact with ASN 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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133B ASP* 3.0 23.8 + - - +
134B ARG* 3.5 17.2 - - - +
135B LEU 3.2 0.2 - - - -
136B MET* 1.3 73.5 - - - +
138B VAL* 1.3 54.5 + - + +
140B SER* 3.2 4.8 + - - -
141B GLU* 2.8 44.7 + - + +
169B ARG* 3.1 25.7 + - - +
199B TYR* 5.5 0.3 + - - -
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Residues in contact with VAL 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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37B ILE* 3.5 38.1 - - + -
40B SER* 5.0 4.0 - - - -
41B LEU* 3.7 18.8 - - + +
120B VAL* 4.3 11.0 - - + -
125B ILE* 3.8 27.4 - - + -
134B ARG 3.1 16.0 + - - +
135B LEU* 3.1 11.6 + - + +
137B ASN* 1.3 74.2 - - + +
139B ILE* 1.3 58.3 + - - +
141B GLU* 3.2 8.2 + - - +
142B SER* 2.8 37.0 + - - +
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Residues in contact with ILE 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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68B LEU* 6.0 0.2 - - + -
70B VAL* 3.4 41.3 - - + -
72B LEU* 3.7 22.9 - - + -
120B VAL* 4.7 11.7 - - + -
122B VAL* 4.9 0.4 - - + -
135B LEU* 3.2 17.2 + - + +
136B MET* 3.6 24.2 - - - +
137B ASN 3.2 0.6 - - - -
138B VAL* 1.3 75.5 - - - +
140B SER* 1.3 63.4 + - - +
142B SER* 3.1 9.8 + - - -
143B VAL* 3.1 22.6 + - + +
163B ILE* 4.6 3.4 - - + +
166B PRO* 4.0 16.4 - - + -
167B VAL* 4.0 21.8 - - + -
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Residues in contact with SER 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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136B MET 3.1 3.2 + - - -
137B ASN* 3.4 8.3 - - - -
139B ILE* 1.3 76.7 - - - +
141B GLU* 1.3 64.6 + - - +
143B VAL* 3.1 4.0 + - - -
144B LYS* 3.1 25.8 + - - +
166B PRO* 2.7 29.7 + - - +
169B ARG* 3.0 32.1 + - - -
170B ALA* 3.3 20.0 - - - +
173B GLU* 5.6 0.9 - - - -
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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
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41B LEU* 3.9 26.5 - - + -
137B ASN* 2.8 28.6 + - + +
138B VAL* 3.2 4.7 + - - +
140B SER* 1.3 75.1 - - - +
142B SER* 1.3 60.8 + - - +
144B LYS* 3.3 28.3 + - - +
145B LEU* 3.1 30.5 + - + +
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Residues in contact with SER 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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41B LEU* 3.5 12.3 - - - +
44B ILE* 4.1 15.8 - - - +
68B LEU* 3.9 8.5 - - - +
120B VAL* 3.7 28.3 - - - +
138B VAL* 2.8 22.8 + - - +
139B ILE 3.1 9.2 + - - -
141B GLU* 1.3 72.9 - - - +
143B VAL* 1.3 64.5 + - - +
145B LEU* 3.3 13.9 + - - +
146B VAL* 3.3 24.8 + - - +
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Residues in contact with VAL 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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68B LEU* 3.9 18.6 - - + -
139B ILE* 3.1 14.6 + - + +
140B SER 3.1 7.6 + - - +
142B SER* 1.3 74.5 - - - +
144B LYS* 1.3 64.5 + - - +
146B VAL* 3.2 8.2 + - - +
147B MET* 3.1 28.1 + - - +
154B PRO* 4.1 12.1 - - + +
156B VAL* 4.4 3.6 - - + -
167B VAL* 4.0 34.3 - - + +
170B ALA* 3.9 17.0 - - + -
171B VAL* 4.0 22.4 - - + -
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Residues in contact with LYS 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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140B SER* 3.1 14.8 + - - +
141B GLU* 3.6 30.8 + - - +
142B SER 3.3 0.2 - - - -
143B VAL* 1.3 75.4 - - - +
145B LEU* 1.3 58.1 + - + +
147B MET* 3.1 10.0 + - - +
148B GLU* 2.9 50.4 + - - +
170B ALA* 3.8 32.1 - - + +
173B GLU* 2.7 37.3 + - - +
174B LYS* 4.5 15.7 - - + +
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Residues in contact with LEU 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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41B LEU* 3.5 45.5 - - + +
44B ILE* 4.3 8.3 - - + -
45B ARG* 4.2 37.2 - - + +
48B ALA* 4.2 6.0 - - - +
141B GLU* 3.1 19.5 + - + +
142B SER* 3.3 13.2 - - - +
144B LYS* 1.3 78.1 - - + +
146B VAL* 1.3 60.1 + - - +
148B GLU* 3.5 24.9 + - - +
149B GLU* 3.7 15.6 + - - +
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Residues in contact with VAL 146 (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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44B ILE* 4.8 3.1 - - + -
48B ALA* 4.5 7.4 - - + -
66B SER* 4.0 16.8 - - - +
68B LEU* 4.4 15.9 - - + -
117B VAL* 3.9 31.0 - - + -
142B SER 3.6 12.8 - - - +
143B VAL 3.2 7.7 + - - +
145B LEU* 1.3 72.5 - - - +
147B MET* 1.3 64.7 + - - +
148B GLU 3.1 2.0 - - - -
149B GLU* 3.2 22.7 + - - +
152B LEU* 3.3 24.5 - - + +
154B PRO* 4.3 24.5 - - + -
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Residues in contact with MET 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 VAL* 3.3 19.5 - - - +
144B LYS* 3.1 9.3 + - - +
146B VAL* 1.3 75.6 - - - +
148B GLU* 1.3 59.5 + - - +
149B GLU 3.5 7.0 + - - -
150B GLU* 4.1 12.1 + - - +
152B LEU 4.0 12.7 - - - +
154B PRO* 3.8 21.8 - - + -
170B ALA 4.4 1.3 - - - +
171B VAL* 3.9 37.5 - - + +
174B LYS* 3.9 29.3 - - + -
175B LEU* 3.9 33.2 - - + -
307B VAL* 5.0 3.8 - - + +
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Residues in contact with GLU 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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144B LYS* 2.9 31.5 + - - +
145B LEU* 3.8 25.9 - - - +
146B VAL 3.1 0.6 - - - -
147B MET* 1.3 76.7 - - - +
149B GLU* 1.3 62.3 + - - +
150B GLU* 3.6 7.3 + - - +
174B LYS* 2.5 41.3 + - - +
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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