Contacts of the helix formed by residues 141 - 153 (chain B) in PDB entry 2VZE
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 LYS 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLN 4.3 8.1 + - - +
140B MET* 1.3 78.4 + - - +
142B SER* 1.3 69.8 + - - +
143B THR 3.3 1.6 - - - +
144B ASP* 2.9 25.9 + - - +
145B ILE* 3.0 12.6 + - - +
166B GLU* 3.8 22.4 + - - +
532B LYS 3.1 24.0 + - - -
533B SER* 3.6 17.4 - - - +
534B VAL* 3.8 13.5 - - - +
535B THR 3.7 26.2 - - - +
537B PRO* 4.9 7.0 - - - +
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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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141B LYS* 1.3 75.0 - - - +
143B THR* 1.3 62.0 + - - +
145B ILE* 3.1 5.0 + - - +
146B LEU* 2.8 30.3 + - - +
166B GLU* 3.2 40.5 + - - +
169B THR* 4.3 12.8 - - - +
170B VAL* 3.8 16.9 - - - +
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Residues in contact with THR 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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141B LYS* 3.3 1.4 - - - +
142B SER* 1.3 82.5 + - - +
144B ASP* 1.3 63.9 + - - +
146B LEU* 3.5 10.8 + - + +
147B TYR* 3.1 24.0 + - + +
170B VAL* 5.5 0.9 - - - -
484B GLU* 6.0 1.8 - - - +
534B VAL* 4.2 17.7 + - - +
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Residues in contact with ASP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B MET* 3.9 18.0 - - + -
141B LYS* 2.9 28.0 + - - +
143B THR* 1.3 78.1 - - - +
145B ILE* 1.3 62.7 + - - +
147B TYR* 3.4 3.9 + - - +
148B ARG* 3.0 48.3 + - - +
534B VAL 4.6 1.4 - - - +
535B THR* 2.9 27.6 + - - -
536B ALA* 3.1 19.4 + - - -
539B LYS* 3.9 8.5 + - - -
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 5.7 1.1 - - + -
140B MET* 3.9 32.5 - - + +
141B LYS 3.0 12.6 + - - +
142B SER* 3.1 6.0 + - - +
144B ASP* 1.3 74.1 - - - +
146B LEU* 1.3 66.2 + - - +
148B ARG* 3.2 4.6 + - - +
149B LEU* 2.9 46.7 + - + +
157B ILE* 4.5 6.1 - - + -
163B VAL* 4.3 9.9 - - + -
166B GLU* 3.7 30.7 - - + -
167B VAL* 3.8 30.3 - - + +
170B VAL* 4.4 7.9 - - + -
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B SER 2.8 19.5 + - - +
143B THR* 3.8 11.0 - - + +
145B ILE* 1.3 73.8 - - - +
147B TYR* 1.3 56.4 - - - +
149B LEU* 3.9 3.0 - - - +
150B GLN* 2.9 69.6 + - - +
170B VAL* 4.0 21.5 - - + +
173B GLU* 3.7 33.7 - - + +
174B CYS* 3.9 19.3 - - - -
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Residues in contact with TYR 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 THR* 3.1 12.8 + - + +
144B ASP* 3.5 9.9 - - - +
146B LEU* 1.3 78.4 - - - +
148B ARG* 1.3 72.4 + - - +
150B GLN* 4.0 4.1 - - - +
151B MET* 2.9 66.9 + - + +
220B PHE* 3.9 17.3 - + - -
227B LEU* 3.3 41.0 + - + +
228B PRO* 2.6 42.9 + - + -
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Residues in contact with ARG 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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134B MET* 5.8 1.1 - - + -
135B PRO 6.0 0.9 - - - -
136B GLY* 5.6 6.2 - - - -
140B MET* 3.6 32.4 - - + +
144B ASP* 3.0 42.6 + - - +
145B ILE* 3.2 3.8 + - - +
147B TYR* 1.3 90.0 - - + +
149B LEU* 1.3 54.1 - - + +
152B SER* 2.6 41.2 + - - -
220B PHE* 3.3 55.0 - - + +
228B PRO* 4.0 21.8 - - - +
477B GLU* 5.6 0.2 + - - -
538B TYR* 4.9 9.9 + - - -
539B LYS* 5.0 8.1 - - - +
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Residues in contact with LEU 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 ALA* 3.9 21.3 - - + -
134B MET* 5.5 0.2 - - + -
145B ILE* 2.9 38.3 + - + +
146B LEU* 5.2 0.4 - - - -
148B ARG* 1.3 78.3 - - + +
150B GLN* 1.3 57.8 + - - +
152B SER* 3.7 2.7 - - - +
153B LYS* 2.9 24.9 + - - -
154B ALA* 3.3 31.4 + - + +
157B ILE* 4.5 11.2 - - + -
167B VAL* 5.4 3.6 - - + -
170B VAL* 5.3 3.8 - - + -
171B ALA* 5.5 1.6 - - - -
174B CYS* 3.9 31.1 - - + +
177B LEU* 4.2 25.1 - - + -
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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 LEU* 2.9 45.1 + - + +
147B TYR* 4.1 3.7 - - - +
149B LEU* 1.3 75.6 - - - +
151B MET* 1.3 64.1 + - - +
152B SER 3.6 0.2 + - - -
153B LYS* 3.6 19.5 + - - +
173B GLU* 3.0 36.7 + - - +
174B CYS* 4.5 7.0 - - - -
175B PRO* 5.3 3.7 - - + +
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Residues in contact with MET 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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108B ARG* 4.6 1.6 + - - -
147B TYR* 2.9 68.6 + - + +
148B ARG 4.2 1.3 - - - +
150B GLN* 1.3 78.0 - - - +
152B SER* 1.3 60.2 + - - +
153B LYS* 3.7 4.3 + - - +
220B PHE* 4.4 7.4 - - + -
228B PRO 4.0 6.7 - - - +
229B LYS* 5.4 2.0 - - - -
230B MET* 3.2 36.8 - - + +
428B ASP* 4.5 6.4 - - - +
429B ASN* 6.3 0.4 - - - -
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Residues in contact with SER 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 2.8 30.9 + - - +
134B MET* 3.2 40.9 - - - +
148B ARG 2.6 24.2 + - - -
149B LEU 3.5 1.0 + - - -
151B MET* 1.3 76.9 - - - +
153B LYS* 1.3 66.6 + - - +
154B ALA* 3.2 10.7 + - - +
220B PHE* 4.4 2.9 - - - -
230B MET* 3.8 16.3 - - - -
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 4.9 5.6 - - - +
149B LEU 2.9 11.2 + - - -
150B GLN* 3.6 15.0 + - - +
151B MET 3.4 3.8 - - - +
152B SER* 1.3 81.9 - - - +
154B ALA* 1.3 69.6 + - - +
155B LYS* 3.4 12.5 + - - +
176B SER* 3.7 30.0 + - - +
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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
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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