Contacts of the helix formed by residues 141 - 155 (chain B) in PDB entry 5VZ4
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 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B ALA 3.4 10.7 + - - +
138B CYS 3.2 9.7 + - - +
139B VAL 4.4 0.2 - - - -
140B GLY* 1.3 78.6 - - - +
142B VAL* 1.3 66.9 + - - +
143B VAL* 3.4 9.6 + - - +
144B CYS* 3.1 29.7 + - + +
145B ASN* 3.0 26.4 + - - +
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Residues in contact with VAL 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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40A GLN* 3.5 37.2 - - + +
140B GLY 4.2 1.0 + - - +
141B ASP* 1.3 79.2 + - - +
143B VAL* 1.3 71.4 + - + +
145B ASN* 3.7 3.8 - - - +
146B ALA* 3.2 19.9 + - + +
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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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141B ASP* 3.4 8.5 + - - +
142B VAL* 1.3 86.0 - - + +
144B CYS* 1.3 62.2 + - - +
146B ALA* 3.3 6.1 + - - +
147B GLN* 2.9 42.8 + - + +
177B ASN 4.4 9.2 - - - +
178B ILE* 5.1 4.3 - - + -
179B PRO* 5.8 4.3 - - + -
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Residues in contact with CYS 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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138B CYS* 2.1 58.6 - - - +
141B ASP* 3.1 17.7 + - + +
143B VAL* 1.3 77.7 - - - +
145B ASN* 1.3 52.2 + - - +
147B GLN* 3.1 1.3 + - - +
148B LEU* 2.6 38.3 + - - +
174B PHE* 4.6 1.8 - - - -
178B ILE* 4.5 18.2 - - + -
179B PRO* 6.5 0.4 - - + -
182B ILE* 3.9 23.6 - - + -
186B LEU* 4.4 7.0 - - - -
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Residues in contact with ASN 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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86A MET* 3.4 24.2 - - - +
87A VAL* 2.8 49.5 + - - +
138B CYS 3.2 7.2 + - - -
139B VAL* 2.8 29.3 + - - +
141B ASP 3.0 20.4 + - - +
142B VAL* 3.7 4.9 - - - +
144B CYS* 1.3 73.3 - - - +
146B ALA* 1.3 57.7 + - - +
148B LEU* 3.3 6.4 + - - +
149B ALA* 2.8 27.4 + - - +
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Residues in contact with ALA 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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84A ASN* 6.2 3.8 - - + -
85A PRO* 4.5 13.9 - - - +
142B VAL* 3.2 13.8 + - + +
143B VAL* 3.3 9.4 + - - +
145B ASN* 1.3 81.0 + - - +
147B GLN* 1.3 65.4 + - + +
149B ALA* 3.3 11.1 + - - +
150B SER* 3.3 16.5 + - - -
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Residues in contact with GLN 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* 2.9 27.0 + - + +
144B CYS 3.8 2.2 - - - +
146B ALA* 1.3 76.4 - - + +
148B LEU* 1.3 67.5 + - - +
150B SER* 3.4 17.5 + - - +
151B TYR* 3.4 8.1 + - - +
173B PHE* 3.6 26.9 - - - -
174B PHE* 3.3 31.7 - - + +
177B ASN* 3.6 38.9 + - - +
178B ILE* 4.0 5.6 - - + -
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Residues in contact with LEU 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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87A VAL* 4.2 9.4 - - + -
98A LEU* 4.6 2.9 - - + -
135B ALA 5.3 0.4 - - - +
138B CYS* 3.9 16.4 - - + -
139B VAL* 4.0 27.6 - - + -
144B CYS 2.6 21.8 + - - +
145B ASN* 3.6 4.0 - - - +
147B GLN* 1.3 73.7 - - - +
149B ALA* 1.3 63.0 + - - +
151B TYR* 3.1 25.6 + - + +
152B LEU* 2.9 40.3 + - + +
174B PHE* 3.5 14.5 - - + -
186B LEU* 5.4 0.4 - - + -
205B LEU* 3.8 30.7 - - + -
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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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85A PRO* 3.8 37.2 - - + +
86A MET 4.3 0.2 - - - +
87A VAL* 3.7 19.2 - - + +
100A THR* 4.1 8.0 + - + -
145B ASN 2.8 16.6 + - - +
146B ALA 3.6 5.8 - - - +
147B GLN 3.2 0.2 - - - -
148B LEU* 1.3 77.2 - - - +
150B SER* 1.3 62.9 + - - +
152B LEU* 3.4 1.1 + - - +
153B LYS* 3.0 29.6 + - - +
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Residues in contact with SER 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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85A PRO* 5.3 6.5 - - - +
146B ALA 3.3 11.5 + - - -
147B GLN* 3.8 15.6 + - - -
148B LEU 3.2 1.0 + - - -
149B ALA* 1.3 76.8 - - - +
151B TYR* 1.3 57.9 + - - +
153B LYS* 3.7 8.3 + - - +
154B ALA* 3.1 28.6 + - - +
170B ALA* 4.2 5.5 - - - +
173B PHE* 5.9 4.9 - - - -
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Residues in contact with TYR 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 GLN 3.4 8.4 + - - +
148B LEU* 3.1 33.5 + - + +
150B SER* 1.3 78.2 - - - +
152B LEU* 1.3 68.6 + - + +
154B ALA* 3.2 1.7 + - - -
155B CYS* 3.1 30.7 + - + +
170B ALA* 4.1 21.1 - - - +
171B ILE* 3.7 22.2 - - + +
174B PHE* 4.2 27.6 - + + -
175B TYR* 5.8 4.3 - + - -
204B ALA 3.6 3.5 + - - -
205B LEU* 2.6 32.0 + - + -
206B HIS* 3.4 1.4 - - - -
207B SER* 3.1 42.7 + - - -
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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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87A VAL* 4.1 18.4 - - + -
98A LEU* 4.4 19.3 - - + +
100A THR* 3.8 22.2 - - - +
148B LEU* 2.9 49.6 + - + +
149B ALA 4.0 0.2 - - - +
151B TYR* 1.3 81.4 - - + +
153B LYS* 1.3 64.2 + - - +
155B CYS* 3.5 4.1 + - + -
156B SER* 3.3 22.0 + - - -
204B ALA* 3.5 32.3 - - + +
207B SER* 6.1 0.9 - - - -
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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
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85A PRO* 4.1 18.6 - - + +
100A THR* 3.6 25.4 - - + -
102A ASP* 3.2 35.1 + - - +
149B ALA 3.0 17.9 + - - +
150B SER* 3.8 6.7 - - - +
152B LEU* 1.3 76.9 - - - +
154B ALA* 1.3 63.3 + - - +
155B CYS 3.0 0.3 + - - -
156B SER* 2.7 25.7 + - - +
166B GLN* 5.4 0.2 - - - -
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Residues in contact with ALA 154 (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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150B SER 3.1 10.5 + - - +
151B TYR 3.2 1.5 + - - +
153B LYS* 1.3 77.5 - - - +
155B CYS* 1.3 57.9 + - - +
156B SER 3.5 2.6 + - - +
162B CYS* 5.0 2.6 - - - +
163B ASP* 4.2 4.9 + - - +
166B GLN* 3.7 39.1 - - + +
167B CYS* 3.6 15.2 + - - +
170B ALA* 3.3 33.9 - - + -
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Residues in contact with CYS 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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151B TYR* 3.1 37.0 + - + +
152B LEU* 3.7 5.6 - - + +
153B LYS 3.0 1.0 - - - -
154B ALA* 1.3 78.4 - - - +
156B SER* 1.3 56.8 + - - +
167B CYS* 2.1 61.0 - - - -
171B ILE* 3.9 1.1 - - - -
207B SER* 3.6 17.6 - - - -
209B THR* 5.5 1.7 + - - -
210B CYS* 3.4 20.8 + - + +
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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