Contacts of the helix formed by residues 131 - 149 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLY 3.8 3.1 + - - +
130A VAL* 1.3 79.0 - - - +
132A ASP* 1.3 52.5 + - - +
133A ASP* 3.6 14.5 + - - +
134A ARG* 3.0 24.0 + - - +
135A LEU* 2.8 32.4 + - - +
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Residues in contact with ASP 132 (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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72A LEU* 5.3 0.3 - - - +
74A HIS* 2.7 39.4 + - - -
75A ASN* 4.0 15.1 + - - +
131A ASP* 1.3 71.2 - - - +
133A ASP* 1.3 56.7 + - - +
135A LEU* 3.1 11.4 + - - +
136A MET* 2.8 40.9 + - - +
197A ASN* 5.9 0.9 - - - -
199A TYR* 3.8 25.5 - - + +
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Residues in contact with ASP 133 (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 ASP* 3.6 14.6 - - - +
132A ASP* 1.3 76.9 - - - +
134A ARG* 1.3 62.6 + - - +
136A MET* 3.3 3.1 + - - +
137A ASN* 3.1 30.5 + - - +
198A LYS* 3.2 18.2 + - - -
199A TYR* 2.4 44.0 + - - +
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Residues in contact with ARG 134 (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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30A GLU* 5.7 1.2 + - - -
33A GLN* 5.0 11.9 + - - +
34A ASN* 2.4 34.2 + - - +
37A ILE* 3.5 41.8 - - + +
130A VAL* 3.6 12.7 - - + +
131A ASP* 3.0 18.8 + - - +
133A ASP* 1.3 72.3 - - - +
135A LEU* 1.3 67.7 + - - +
137A ASN* 3.0 21.7 + - - +
138A VAL* 2.9 26.6 + - + +
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Residues in contact with LEU 135 (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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72A LEU* 3.8 11.7 - - + -
74A HIS* 3.7 29.6 - - + +
120A VAL* 5.4 0.4 - - + -
122A VAL* 3.9 20.6 - - + -
125A ILE* 3.7 37.7 - - + -
126A ARG* 4.0 11.2 - - + -
130A VAL* 4.0 5.3 - - + +
131A ASP 2.8 15.3 + - - +
132A ASP* 3.1 14.8 + - - +
134A ARG* 1.3 75.7 - - - +
136A MET* 1.3 58.0 + - - +
138A VAL* 3.0 12.3 + - + +
139A ILE* 3.0 37.2 + - + +
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Residues in contact with MET 136 (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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72A LEU* 4.6 5.6 - - + -
75A ASN* 3.6 27.6 - - - +
132A ASP* 2.8 21.9 + - + +
133A ASP 3.7 4.5 - - - +
135A LEU* 1.3 74.0 - - + +
137A ASN* 1.3 55.7 + - - +
139A ILE* 3.2 19.7 + - - +
140A SER 3.0 23.6 + - - -
162A SER* 3.6 30.5 - - - +
163A ILE* 4.5 0.9 - - - +
165A TYR* 5.9 0.2 - - + -
166A PRO* 3.4 33.0 - - + +
169A ARG* 3.4 13.0 + - - +
199A TYR* 3.4 43.1 - - + +
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Residues in contact with ASN 137 (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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133A ASP* 3.1 21.4 + - - +
134A ARG* 3.0 25.2 + - - +
136A MET* 1.3 72.6 - - - +
138A VAL* 1.3 53.5 + - + +
140A SER* 3.1 5.2 + - - -
141A GLU* 2.7 46.9 + - + +
169A ARG* 3.1 26.1 + - - +
199A TYR* 5.7 0.2 + - - -
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Residues in contact with VAL 138 (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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37A ILE* 3.9 34.1 - - + -
40A SER* 5.0 3.8 - - - -
41A LEU* 3.6 23.6 - - + -
120A VAL* 4.6 6.3 - - + -
125A ILE* 3.8 26.5 - - + -
134A ARG* 2.9 25.0 + - + +
135A LEU* 3.0 11.4 + - + +
137A ASN* 1.3 74.6 - - + +
139A ILE* 1.3 54.2 + - - +
141A GLU* 3.1 8.6 + - - +
142A SER* 2.8 43.3 + - - +
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Residues in contact with ILE 139 (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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68A LEU* 4.8 0.3 - - - +
70A VAL* 3.4 41.7 - - + -
72A LEU* 3.8 15.0 - - + -
120A VAL* 4.6 13.9 - - + -
122A VAL* 5.0 0.7 - - + -
135A LEU* 3.0 22.3 + - + +
136A MET* 3.2 32.5 + - - +
138A VAL* 1.3 74.9 - - - +
140A SER* 1.3 61.0 - - - +
142A SER* 3.3 7.2 + - - -
143A VAL* 3.1 27.5 + - + +
163A ILE* 4.5 4.3 - - + +
166A PRO* 3.9 17.9 - - + -
167A VAL* 4.2 18.6 - - + -
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A MET 3.0 5.7 + - - -
137A ASN* 3.3 9.0 - - - -
139A ILE* 1.3 71.2 - - - +
141A GLU* 1.3 67.6 + - - +
143A VAL* 3.1 11.6 + - - -
144A LYS* 3.1 20.8 + - - +
166A PRO* 2.9 24.2 + - - +
169A ARG* 3.1 31.7 + - - -
170A ALA* 3.5 19.1 - - - +
173A GLU* 5.4 3.8 - - - -
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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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41A LEU* 4.1 26.1 - - + +
137A ASN* 2.7 30.2 + - + +
138A VAL* 3.5 6.5 - - - +
140A SER* 1.3 71.7 - - - +
142A SER* 1.3 62.1 + - - +
144A LYS* 3.1 26.5 + - - +
145A LEU* 3.1 22.9 + - + +
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Residues in contact with SER 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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40A SER 5.7 0.3 - - - -
41A LEU* 3.5 15.1 - - - +
44A ILE* 4.0 15.5 - - - +
68A LEU* 3.9 6.5 - - - +
120A VAL* 3.7 29.5 - - - +
138A VAL* 2.8 28.3 + - - +
139A ILE 3.5 5.2 - - - -
141A GLU* 1.3 72.5 - - - +
143A VAL* 1.3 61.3 + - - +
145A LEU* 3.3 26.0 + - - +
146A VAL* 3.6 12.3 - - - +
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Residues in contact with VAL 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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68A LEU* 3.8 19.5 - - + -
139A ILE* 3.1 14.9 + - + +
140A SER 3.1 8.4 + - - +
142A SER* 1.3 73.4 - - - +
144A LYS* 1.3 64.4 + - - +
146A VAL* 3.1 16.4 + - - +
147A MET* 3.2 26.4 + - - +
154A PRO* 4.1 11.7 - - + -
156A VAL* 4.3 4.3 - - + -
167A VAL* 4.0 33.9 - - + +
170A ALA* 3.7 17.7 - - + -
171A VAL* 4.1 12.8 - - + -
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Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A SER* 3.1 17.4 + - - +
141A GLU* 3.1 18.5 + - - +
143A VAL* 1.3 76.3 - - - +
145A LEU* 1.3 53.6 + - + +
147A MET* 3.8 9.1 - - - +
148A GLU* 2.7 55.1 + - + +
170A ALA* 3.5 31.9 - - + +
173A GLU* 2.9 38.3 + - - +
174A LYS* 4.3 17.1 - - + +
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.7 40.2 - - + +
44A ILE* 4.4 11.7 - - + -
45A ARG* 4.3 37.3 - - + +
48A ALA* 4.0 6.7 - - - +
141A GLU* 3.1 24.0 + - + +
142A SER* 3.4 18.8 - - - +
143A VAL 3.1 1.0 - - - -
144A LYS* 1.3 75.0 - - + +
146A VAL* 1.3 63.8 + - - +
148A GLU* 3.6 22.6 + - + +
149A GLU* 3.5 22.3 + - - +
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Residues in contact with VAL 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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44A ILE* 4.5 3.8 - - + -
48A ALA* 4.5 6.7 - - + -
66A SER* 3.7 35.4 - - - +
68A LEU* 4.4 12.6 - - + -
117A VAL* 3.8 28.0 - - + -
142A SER 3.6 15.3 - - - +
143A VAL* 3.1 7.4 + - - +
145A LEU* 1.3 79.1 - - - +
147A MET* 1.3 61.4 + - - +
149A GLU* 3.3 9.2 + - - +
152A LEU* 3.2 33.9 - - + +
154A PRO* 4.2 17.5 - - + -
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Residues in contact with MET 147 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A VAL* 3.2 21.9 + - - +
144A LYS* 3.8 7.9 - - - +
146A VAL* 1.3 70.1 - - - +
148A GLU* 1.3 55.1 + - - +
149A GLU 2.9 21.1 + - - -
150A GLU* 3.7 6.2 + - - +
152A LEU 4.1 11.2 - - - +
154A PRO* 3.9 21.3 - - + -
170A ALA 4.4 0.9 - - - +
171A VAL* 3.9 38.8 - - + -
174A LYS* 3.6 41.0 - - + -
175A LEU* 4.0 22.7 - - + -
307A VAL* 5.0 3.4 - - + +
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Residues in contact with GLU 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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144A LYS* 2.7 39.0 + - + +
145A LEU* 3.9 24.7 - - + +
146A VAL 3.4 0.2 - - - -
147A MET* 1.3 69.9 - - - +
149A GLU* 1.3 59.0 - - - +
150A GLU* 3.6 5.3 + - - +
174A LYS* 3.4 28.5 + - - +
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Residues in contact with GLU 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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45A ARG* 4.2 9.7 - - - +
48A ALA* 3.4 24.1 - - + +
49A LYS* 3.4 34.0 + - - +
52A GLY* 4.3 8.1 - - - -
56A ARG* 4.5 12.4 + - - +
145A LEU 3.5 10.3 + - - +
146A VAL 3.3 8.7 + - - +
147A MET 2.9 4.9 + - - -
148A GLU* 1.3 76.9 - - - +
150A GLU* 1.3 67.6 + - - +
152A LEU* 3.1 31.8 + - + +
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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