Contacts of the helix formed by residues 164 - 180 (chain A) in PDB entry 2V5E
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ALA 3.2 12.9 + - - +
161A CYS 3.0 6.1 + - - +
162A ASN 4.9 0.2 - - - -
163A LEU* 1.3 81.0 - - - +
165A ASP* 1.3 65.8 + - - +
166A THR* 3.2 13.7 + - - -
167A CYS* 2.9 29.2 + - + +
168A LYS* 3.0 27.4 + - - +
203A VAL* 5.4 0.5 - - - +
204A PRO* 5.5 0.9 - - - +
207A HIS* 3.8 29.7 + - + +
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Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU 4.2 2.0 + - - +
164A ASP* 1.3 73.4 + - - +
166A THR* 1.3 64.4 + - - +
168A LYS* 4.0 22.5 + - - +
169A LYS* 3.3 28.5 + - - +
109B ASP* 4.6 4.0 - - - +
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Residues in contact with THR 166 (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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164A ASP* 3.2 10.6 + - - -
165A ASP* 1.3 76.7 - - - +
167A CYS* 1.3 66.4 + - - +
169A LYS* 3.4 9.9 + - - +
170A TYR* 3.1 50.2 + - + -
202A LYS 4.0 17.9 - - - +
203A VAL* 4.2 5.6 - - + -
204A PRO* 4.4 11.4 - - + -
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Residues in contact with CYS 167 (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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161A CYS* 2.0 56.1 - - - +
164A ASP* 2.9 18.4 + - + +
166A THR* 1.3 73.0 - - - +
168A LYS* 1.3 55.2 + - - +
170A TYR* 3.9 0.2 - - - -
171A ARG* 2.8 36.4 + - - +
199A PHE* 3.8 21.4 - - - -
203A VAL* 3.8 17.7 - - + +
207A HIS* 3.8 22.2 - - + -
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Residues in contact with LYS 168 (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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161A CYS* 3.1 16.6 + - - +
162A ASN* 3.5 27.8 + - - +
164A ASP 3.0 17.1 + - - +
165A ASP* 4.0 24.0 + - - +
167A CYS* 1.3 74.4 - - - +
169A LYS* 1.3 61.5 + - - +
171A ARG* 3.5 2.1 + - - +
172A SER* 3.1 28.2 + - - -
108B ASP* 4.5 16.4 - - - +
109B ASP* 4.1 34.5 + - - +
110B ASP 3.8 9.9 - - - +
111B LEU* 3.9 23.6 - - + -
112B SER* 5.0 0.3 + - - -
126B HIS* 6.0 0.7 - - - +
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Residues in contact with LYS 169 (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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165A ASP* 3.3 19.9 + - - +
166A THR* 3.7 7.9 + - - +
167A CYS 3.3 0.2 - - - -
168A LYS* 1.3 79.0 - - - +
170A TYR* 1.3 87.8 + - + +
172A SER* 3.4 3.7 + - - -
173A ALA* 2.9 29.3 + - + +
109B ASP* 3.3 40.8 + - + +
110B ASP 4.7 2.2 - - - -
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Residues in contact with TYR 170 (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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166A THR* 3.1 38.9 + - + -
169A LYS* 1.3 104.2 - - + +
171A ARG* 1.3 65.2 + - - +
173A ALA* 3.6 12.8 - - + +
174A TYR* 3.3 24.6 + - - +
195A ALA 4.8 1.1 - - - +
198A GLN* 4.1 31.0 - - + -
199A PHE* 3.6 10.6 - - + +
202A LYS* 3.7 31.4 - - + +
203A VAL* 3.5 23.8 - - + -
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Residues in contact with ARG 171 (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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158A ALA* 4.0 6.7 + - - +
161A CYS* 4.1 12.6 - - - -
162A ASN* 3.0 27.5 + - - +
167A CYS 2.8 18.5 + - - +
168A LYS 3.7 4.0 - - - +
170A TYR* 1.3 73.0 - - - +
172A SER* 1.3 60.5 + - - +
174A TYR* 3.0 26.9 + - + +
175A ILE* 2.8 35.1 + - + +
199A PHE* 3.5 9.5 - - + -
211A MET* 3.6 29.4 - - - +
224A ARG* 4.1 3.6 - - - +
61B GLU* 2.8 41.2 + - - -
112B SER* 3.2 23.1 + - - +
113B PHE* 4.0 2.2 - - - +
114B LEU* 4.0 8.1 - - - +
120B TYR* 4.2 16.7 + - - -
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Residues in contact with SER 172 (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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168A LYS 3.1 12.4 + - - -
169A LYS* 3.8 4.5 - - - -
171A ARG* 1.3 73.7 - - - +
173A ALA* 1.3 58.1 + - - +
175A ILE* 4.4 0.4 - - - -
176A THR* 3.0 36.7 + - - -
110B ASP* 2.8 50.0 + - - -
111B LEU 3.6 0.2 - - - -
112B SER* 3.3 27.5 + - - -
122B ILE* 4.7 3.8 - - - -
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Residues in contact with ALA 173 (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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169A LYS* 2.9 21.0 + - + +
170A TYR* 3.6 20.2 - - + +
171A ARG 3.2 0.2 - - - -
172A SER* 1.3 77.2 - - - +
174A TYR* 1.3 56.8 + - - +
176A THR* 5.1 1.6 - - - -
177A PRO* 3.0 19.2 - - - +
195A ALA* 3.3 14.2 - - + +
198A GLN* 6.1 1.1 - - - +
1354A EDO 4.6 8.6 - - - +
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Residues in contact with TYR 174 (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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170A TYR 3.3 21.0 + - - +
171A ARG* 3.0 27.0 + - + +
173A ALA* 1.3 77.6 - - - +
175A ILE* 1.3 84.8 + - + +
176A THR 3.2 2.0 + - - -
177A PRO* 3.4 1.1 - - - +
178A CYS* 3.0 36.6 + - - -
195A ALA* 3.4 33.0 - - + +
196A LEU* 3.5 25.8 - - + +
199A PHE* 3.7 38.1 - + + -
200A PHE* 6.0 0.7 - + - -
211A MET* 5.3 2.8 - - - +
228A THR* 2.6 42.0 + - + +
230A VAL* 3.9 4.5 - - + -
120B TYR* 4.8 1.0 + - - -
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Residues in contact with ILE 175 (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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171A ARG* 2.8 32.1 + - + +
172A SER 4.1 2.9 - - - +
174A TYR* 1.3 98.3 - - + +
176A THR* 1.3 57.0 + - - +
178A CYS* 4.6 1.6 - - - -
179A THR* 2.7 37.0 + - + +
230A VAL* 3.7 13.2 - - + -
112B SER* 3.6 21.8 - - - +
120B TYR* 3.6 51.4 - - + -
122B ILE* 3.7 21.1 - - + -
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Residues in contact with THR 176 (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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172A SER 3.0 17.6 + - - -
173A ALA* 4.6 1.6 - - - -
174A TYR 3.2 0.2 - - - -
175A ILE* 1.3 80.1 - - - +
177A PRO* 1.4 71.8 - - + +
179A THR* 3.5 1.4 + - - -
180A THR* 2.7 33.6 + - - +
110B ASP* 4.8 2.9 + - - -
122B ILE* 3.7 15.7 - - + +
124B ARG* 2.9 32.5 + - - +
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Residues in contact with PRO 177 (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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173A ALA 3.0 28.5 - - - +
174A TYR 3.4 6.3 - - - +
176A THR* 1.4 92.6 - - + +
178A CYS* 1.3 59.9 + - - +
179A THR 3.3 0.7 + - - -
180A THR* 3.6 20.3 + - - +
187A CYS* 3.9 8.3 - - - +
188A ASN* 4.3 6.1 + - + +
191A LYS* 3.8 43.5 - - + +
192A CYS* 4.3 4.1 - - - +
195A ALA* 3.9 5.6 - - + -
1354A EDO 3.9 6.3 - - - +
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Residues in contact with CYS 178 (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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174A TYR* 3.0 40.1 + - - +
175A ILE 4.1 1.3 - - - +
177A PRO* 1.3 77.9 - - - +
179A THR* 1.3 58.1 + - - +
180A THR 3.7 0.2 - - - -
186A VAL 5.1 0.2 - - - +
187A CYS* 3.9 3.7 - - - +
192A CYS* 2.0 59.2 - - - -
196A LEU* 4.3 3.1 - - - -
230A VAL* 3.6 29.9 - - + +
233A CYS* 3.2 22.3 - - - +
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Residues in contact with THR 179 (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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175A ILE* 2.7 28.5 + - + +
176A THR 3.5 3.5 + - - -
178A CYS* 1.3 81.5 - - - +
180A THR* 1.3 62.3 + - - +
181A SER* 3.5 4.6 + - - -
186A VAL 4.9 4.6 - - - +
230A VAL* 4.1 16.2 - - + -
120B TYR* 4.0 29.1 + - + +
122B ILE* 4.2 8.7 - - - +
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Residues in contact with THR 180 (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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176A THR* 2.7 31.8 + - - +
177A PRO* 3.6 11.2 + - - +
178A CYS 3.7 0.2 - - - -
179A THR* 1.3 76.1 + - - +
181A SER* 1.3 70.2 + - - +
182A MET* 3.8 3.1 + - + +
186A VAL 4.0 1.6 - - - -
187A CYS* 3.5 15.2 - - - -
188A ASN 4.1 2.9 + - - -
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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