Contacts of the helix formed by residues 163 - 176 (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 ILE 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A VAL* 3.4 34.3 - - + +
72A LEU* 4.0 25.1 - - + -
136A MET* 4.7 1.6 - - - -
139A ILE* 4.6 3.4 - - + -
156A VAL* 3.4 27.6 - - + -
158A GLY* 3.4 33.2 - - - -
160A ASP 3.4 15.3 - - - +
161A HIS 3.0 2.0 - - - -
162A SER* 1.3 76.6 - - - +
164A SER* 1.3 64.4 + - - +
166A PRO* 3.1 21.9 - - - +
167A VAL* 3.2 15.6 - - + +
310A ASP* 5.5 0.9 - - - -
312A VAL* 4.0 12.8 - - + -
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Residues in contact with SER 164 (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 HIS* 3.2 30.9 + - - -
162A SER 3.1 0.8 + - - -
163A ILE* 1.3 76.1 - - - +
165A TYR* 1.3 59.1 + - - +
167A VAL* 4.4 3.6 - - - -
168A VAL* 2.9 38.9 + - - +
204A SER* 4.5 1.8 - - - -
205A PHE* 4.4 12.3 - - - -
208A ILE* 4.1 6.3 - - - -
268A SER* 3.5 2.1 + - - -
310A ASP* 2.5 33.6 + - - -
312A VAL* 4.4 2.1 - - - +
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Residues in contact with TYR 165 (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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162A SER 3.3 7.2 + - - +
163A ILE 3.3 0.2 - - - -
164A SER* 1.3 75.9 - - - +
166A PRO* 1.3 69.8 - - + +
168A VAL* 3.8 0.7 - - - +
169A ARG* 2.8 56.9 + - + +
199A TYR* 3.9 31.0 - + - -
204A SER* 3.9 18.4 - - - +
207A ARG* 3.5 49.3 + - + -
208A ILE* 3.8 19.1 - - + +
213A TYR* 4.2 18.3 + + - -
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Residues in contact with PRO 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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136A MET* 3.4 43.5 - - + +
139A ILE* 3.9 13.2 - - + -
140A SER* 2.9 31.0 + - - +
162A SER 3.4 8.1 - - - +
163A ILE* 3.1 16.6 - - - +
165A TYR* 1.3 103.9 - - + +
167A VAL* 1.3 54.8 + - - +
169A ARG* 3.9 12.8 - - + +
170A ALA* 3.0 21.8 + - - +
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 5.1 0.2 - - + -
139A ILE* 4.2 11.0 - - + -
143A VAL* 4.0 24.0 - - + +
154A PRO* 5.8 2.0 - - + +
156A VAL* 3.7 39.0 - - + -
163A ILE* 3.2 22.0 + - + +
164A SER* 3.9 3.4 - - - +
166A PRO* 1.3 74.5 - - - +
168A VAL* 1.3 58.2 + - - +
170A ALA* 3.2 4.0 + - - +
171A VAL* 3.0 30.1 + - + +
266A TYR* 3.1 35.9 - - + +
309A ALA 5.3 0.2 - - - +
310A ASP* 5.6 0.4 - - - +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER* 2.9 25.4 + - - +
165A TYR 4.0 1.6 - - - +
167A VAL* 1.3 68.1 - - - +
169A ARG* 1.3 67.9 + - - +
171A VAL* 3.2 7.0 + - + +
172A SER* 2.9 24.1 + - - -
179A VAL* 4.7 9.6 - - + -
181A ILE* 4.0 13.0 - - + -
205A PHE* 5.9 0.7 - - + -
208A ILE* 3.8 28.5 - - + -
213A TYR* 3.8 23.1 - - + -
266A TYR* 3.6 38.1 - - + -
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Residues in contact with ARG 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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136A MET* 3.4 20.8 + - - +
137A ASN* 3.1 27.5 + - - +
140A SER* 3.1 26.0 + - - -
165A TYR* 2.8 48.6 + - + +
166A PRO* 3.5 10.1 - - - +
168A VAL* 1.3 76.6 - - - +
170A ALA* 1.3 57.2 + - - +
172A SER* 3.8 1.2 - - - -
173A GLU* 2.9 54.0 + - - +
199A TYR* 5.1 6.3 + - - -
213A TYR* 3.5 40.2 - - + +
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Residues in contact with ALA 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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140A SER* 3.5 29.2 - - - +
143A VAL* 3.7 15.9 - - + -
144A LYS* 3.5 20.0 - - + +
147A MET* 4.6 1.3 - - - -
166A PRO 3.0 17.5 + - - +
167A VAL 3.2 5.4 + - - +
169A ARG* 1.3 76.5 - - - +
171A VAL* 1.3 62.4 + - - +
173A GLU* 4.0 1.6 - - - -
174A LYS* 3.0 28.7 + - - +
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Residues in contact with VAL 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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143A VAL* 4.1 9.4 - - + -
147A MET* 3.9 24.5 - - + -
154A PRO* 4.2 13.5 - - + -
167A VAL* 3.0 21.8 + - + +
168A VAL* 3.9 5.6 - - + +
170A ALA* 1.3 74.7 - - - +
172A SER* 1.3 63.3 + - - +
174A LYS* 3.8 0.9 - - - +
175A LEU* 3.0 37.7 + - + +
179A VAL* 4.9 7.2 - - + -
266A TYR* 4.6 17.9 - - + -
307A VAL* 3.6 34.3 - - + +
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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 VAL* 2.9 17.8 + - - -
171A VAL* 1.3 77.4 - - - +
173A GLU* 1.3 56.2 + - - +
175A LEU* 3.2 3.0 + - - -
176A GLY 2.8 25.5 + - - -
177A GLY 2.6 35.0 + - - +
179A VAL* 5.2 7.3 - - - +
212A GLY 4.8 0.3 + - - -
213A TYR* 3.5 42.0 - - - -
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Residues in contact with GLU 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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140A SER* 5.4 2.8 - - - -
144A LYS* 2.9 30.9 + - - +
169A ARG* 2.9 50.8 + - + +
170A ALA* 4.0 1.3 - - - +
172A SER* 1.3 71.6 - - - +
174A LYS* 1.3 63.7 + - - +
176A GLY* 3.2 15.4 + - - +
213A TYR* 4.4 13.1 + - + -
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Residues in contact with LYS 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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144A LYS* 4.3 17.7 - - + +
147A MET* 3.6 33.2 - - + -
148A GLU* 3.4 45.7 + - + +
170A ALA 3.0 18.7 + - - +
171A VAL 3.8 3.1 - - - +
173A GLU* 1.3 78.6 - - - +
175A LEU* 1.3 62.0 + - + +
176A GLY 3.5 0.3 + - - -
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Residues in contact with LEU 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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147A MET* 4.0 16.8 - - + -
171A VAL* 3.0 28.6 + - + +
172A SER* 3.6 3.1 - - - +
174A LYS* 1.3 77.7 - - + +
176A GLY* 1.3 63.0 + - - +
177A GLY 3.7 0.2 - - - -
179A VAL* 4.7 2.7 - - + -
263A LYS* 3.3 46.3 - - + +
307A VAL* 3.7 41.7 - - + -
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Residues in contact with GLY 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 2.8 9.4 + - - -
173A GLU* 3.2 13.7 + - - -
174A LYS 3.3 1.0 + - - -
175A LEU* 1.3 78.8 - - - +
177A GLY* 1.3 55.0 + - - -
263A LYS* 3.9 9.8 + - - -
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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