Contacts of the helix formed by residues 133 - 152 (chain B) in PDB entry 6NSV
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 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 3.2 29.3 + - - +
132B GLY* 1.3 70.5 - - - -
134B ASP* 1.3 56.5 + - - +
135B ILE 3.3 2.9 - - - -
136B PRO* 3.5 23.7 - - - +
137B SER* 2.7 60.6 + - - +
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Residues in contact with ASP 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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40A ARG* 2.8 45.4 + - - +
98B PHE* 4.3 4.0 - - - -
131B PHE* 3.0 27.9 + - + +
132B GLY 3.3 0.4 - - - -
133B ASP* 1.3 77.5 + - - +
135B ILE* 1.3 62.4 + - - +
137B SER* 3.8 4.9 - - - -
138B ALA* 3.2 22.9 + - - +
637D LEU* 3.8 26.6 + - + +
638D TRP* 3.9 12.3 + - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 4.3 5.4 - - + -
98B PHE* 4.1 24.5 - - + -
117B LEU* 3.6 26.7 - - + +
120B ALA* 4.0 29.6 - - + +
121B TYR* 3.7 21.3 - - + -
124B ALA* 4.2 5.8 - - + -
131B PHE* 4.2 28.4 + - + -
132B GLY 4.7 0.4 + - - -
134B ASP* 1.3 77.3 - - + +
136B PRO* 1.3 72.0 - - + +
138B ALA* 3.1 3.8 + - - +
139B LEU* 2.9 23.7 + - + +
637D LEU* 4.8 5.8 - - + -
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Residues in contact with PRO 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B TYR* 3.8 26.0 - - + -
132B GLY 4.2 6.3 - - - +
133B ASP* 3.4 33.7 - - - +
135B ILE* 1.3 95.1 - - + +
137B SER* 1.3 54.4 + - - +
139B LEU* 3.3 12.2 + - + +
140B ARG* 2.9 30.1 + - - +
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Residues in contact with SER 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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40A ARG 4.4 15.1 + - - -
41A LYS* 4.9 1.6 + - - +
42A TYR* 6.2 2.2 - - - -
133B ASP* 2.7 48.2 + - - +
134B ASP* 3.8 6.3 - - - -
136B PRO* 1.3 73.6 - - - +
138B ALA* 1.3 62.3 + - - +
140B ARG* 3.2 7.2 + - - +
141B ILE* 2.9 35.3 + - - +
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Residues in contact with ALA 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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98B PHE* 3.8 12.8 - - + -
102B GLN* 3.4 28.7 - - - +
105B LEU* 4.9 2.2 - - - +
117B LEU* 3.8 8.7 - - + +
134B ASP 3.2 14.8 + - - +
135B ILE 3.1 5.6 + - - +
137B SER* 1.3 78.5 - - - +
139B LEU* 1.3 58.0 + - - +
141B ILE* 3.4 11.7 + - - +
142B ALA* 2.8 30.1 + - - +
638D TRP* 5.6 1.3 - - + -
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Residues in contact with LEU 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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114B ILE* 3.8 26.7 - - + +
117B LEU* 3.7 33.2 - - + +
118B GLN* 3.6 32.8 - - + +
121B TYR* 4.6 8.7 - - + -
135B ILE* 2.9 19.2 + - + +
136B PRO* 3.6 13.9 - - + +
137B SER 3.3 0.2 - - - -
138B ALA* 1.3 72.3 - - - +
140B ARG* 1.3 61.0 + - - +
142B ALA* 3.2 1.4 + - - +
143B LYS* 2.8 47.7 + - + +
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Residues in contact with ARG 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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43A PRO* 6.4 2.2 - - + -
136B PRO 2.9 17.7 + - - +
137B SER* 3.5 7.0 - - - +
139B LEU* 1.3 77.4 - - - +
141B ILE* 1.3 64.7 + - + +
143B LYS* 3.2 7.8 + - - +
144B LYS* 2.9 24.5 + - - +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 4.8 13.7 - - + -
43A PRO* 5.0 12.1 - - + -
72A LYS 3.6 20.2 - - - +
73A MET* 3.4 45.1 - - + +
74A GLN* 4.1 13.7 - - + -
203A 1PE 5.6 1.6 - - - +
105B LEU* 4.6 5.4 - - + -
137B SER* 2.9 26.7 + - - +
138B ALA* 3.7 9.2 - - - +
140B ARG* 1.3 76.2 - - + +
142B ALA* 1.3 61.4 + - - +
144B LYS* 3.2 6.6 + - - +
145B LYS* 2.8 27.9 + - + +
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Residues in contact with ALA 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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105B LEU* 4.0 25.9 - - + +
110B TYR* 4.6 1.7 - - + -
113B ALA* 5.2 1.8 - - + -
114B ILE* 4.0 19.2 - - + +
117B LEU* 3.9 19.5 - - + -
138B ALA 2.8 21.6 + - - +
139B LEU 3.6 3.8 - - - +
141B ILE* 1.3 75.4 - - - +
143B LYS* 1.3 58.4 + - - +
145B LYS* 3.3 2.1 + - - +
146B ARG* 2.9 29.5 + - - +
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Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 4.2 25.1 - - + -
118B GLN* 4.1 23.7 - - - +
139B LEU* 2.8 35.9 + - + +
140B ARG* 3.8 6.1 - - - +
142B ALA* 1.3 71.7 - - - +
144B LYS* 1.3 57.0 + - - +
146B ARG* 3.6 10.5 + - - +
147B TRP* 3.1 26.9 + - - +
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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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73A MET* 5.7 0.6 - - - +
75A GLN* 3.4 27.9 + - - +
140B ARG 2.9 18.1 + - - +
141B ILE* 3.7 5.8 - - - +
143B LYS* 1.3 75.6 - - - +
145B LYS* 1.3 60.3 + - - +
147B TRP* 3.3 13.8 + - + +
148B ASN* 3.0 54.7 + - - +
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Residues in contact with LYS 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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73A MET 4.9 2.0 + - - +
74A GLN* 2.7 43.4 + - + +
75A GLN* 4.9 7.8 - - + +
76A HIS* 3.9 16.9 + - - +
78A GLN* 5.7 1.3 - - - -
105B LEU* 4.4 10.3 + - + -
108B GLU* 5.2 4.6 + - - +
110B TYR* 3.6 33.6 + - + -
141B ILE 2.8 17.1 + - - +
142B ALA 3.8 3.1 - - - +
144B LYS* 1.3 73.8 - - - +
146B ARG* 1.3 67.0 + - - +
148B ASN* 3.3 16.8 + - + +
149B SER* 3.1 23.6 + - - +
152B GLU* 5.8 3.1 - - - -
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Residues in contact with ARG 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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110B TYR* 3.7 25.6 - - + -
111B ASP* 2.8 30.4 + - - -
114B ILE* 3.5 20.0 - - + -
142B ALA 2.9 17.9 + - - +
143B LYS* 3.6 8.2 + - - +
144B LYS 3.3 0.2 - - - -
145B LYS* 1.3 75.5 - - - +
147B TRP* 1.3 68.8 + - - +
149B SER* 2.4 26.8 + - - +
150B ILE* 3.1 35.6 + - + +
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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
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143B LYS 3.1 14.8 + - - +
144B LYS* 3.8 14.4 - - + +
146B ARG* 1.3 84.7 - - - +
148B ASN* 1.3 70.1 + - - +
150B ILE* 3.0 37.6 + - + +
151B GLU* 2.8 62.5 + - + +
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Residues in contact with ASN 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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75A GLN* 4.1 16.8 - - - +
78A GLN* 5.1 10.9 - - - +
144B LYS* 3.0 58.3 + - - +
145B LYS* 3.7 16.4 - - + +
146B ARG 3.3 0.2 - - - -
147B TRP* 1.3 78.3 - - - +
149B SER* 1.3 61.3 + - - +
151B GLU* 3.2 22.9 - - - +
152B GLU* 3.1 35.4 + - - +
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Residues in contact with SER 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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110B TYR* 3.5 28.8 - - - -
145B LYS* 3.1 12.9 + - - +
146B ARG* 2.4 24.1 + - - +
148B ASN* 1.3 75.2 - - - +
150B ILE* 1.3 67.2 + - - +
152B GLU* 3.0 30.3 + - - +
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Residues in contact with ILE 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 ARG* 3.5 52.5 - - + +
147B TRP* 3.0 34.1 + - + +
149B SER* 1.3 82.4 + - - +
151B GLU* 1.3 66.5 + - - +
152B GLU 3.2 4.7 + - - -
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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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147B TRP* 2.8 55.3 + - + +
148B ASN* 3.2 32.8 - - - +
150B ILE* 1.3 78.3 - - - +
152B GLU* 1.3 62.4 + - + +
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Residues in contact with GLU 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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77A GLU* 3.9 21.2 - - - +
78A GLN* 5.2 6.2 + - - -
145B LYS* 5.8 3.6 - - - -
148B ASN* 3.1 25.2 + - - +
149B SER* 3.0 22.7 + - - +
150B ILE 3.8 4.3 - - - -
151B GLU* 1.3 81.5 - - + +
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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
------------------------------------------------------------
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