Contacts of the helix formed by residues 167 - 179 (chain A) in PDB entry 2P2F
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 SER 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A TYR* 4.9 0.4 - - - -
165A GLY 3.7 1.4 + - - -
166A PHE* 1.3 74.4 - - - +
168A PRO* 1.3 73.4 - - - +
170A ALA 3.0 14.0 + - - -
171A VAL* 3.0 21.3 + - - +
201A ASN* 5.0 0.9 - - - +
584A ARG 3.6 14.8 - - - -
585A LYS* 2.8 30.7 + - - -
586A GLU 3.4 1.7 + - - -
587A ILE 2.8 24.6 + - - -
588A GLY* 4.2 0.8 - - - -
589A PRO* 5.9 0.9 - - - -
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Residues in contact with PRO 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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167A SER* 1.3 86.6 - - - +
169A GLU* 1.3 58.1 + - - +
171A VAL* 3.1 5.0 + - + -
172A ALA* 2.9 27.9 + - - +
201A ASN* 3.7 37.0 - - - +
204A ASP* 3.7 37.0 - - + +
205A ALA* 3.3 18.2 - - + +
585A LYS* 4.8 4.7 - - + +
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Residues in contact with GLU 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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167A SER* 3.3 0.6 + - - -
168A PRO* 1.3 79.0 - - - +
170A ALA* 1.3 62.8 + - - +
172A ALA* 3.6 5.5 + - - +
173A GLY* 3.3 18.5 + - - -
208A ASN* 4.4 17.1 + - - -
585A LYS* 3.5 20.1 + - + +
586A GLU* 3.3 38.6 - - - +
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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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166A PHE* 3.7 22.2 - - + -
167A SER* 3.0 19.3 + - - +
169A GLU* 1.3 77.6 - - - +
171A VAL* 1.3 68.1 + - - +
173A GLY* 3.5 2.1 + - - -
174A ARG* 3.2 38.3 + - - +
586A GLU 4.3 2.5 - - - +
587A ILE* 3.6 21.5 - - + +
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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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138A TYR* 3.4 49.8 - - + +
162A ILE* 3.9 21.3 - - + -
166A PHE* 4.2 2.0 - - + +
167A SER 3.0 18.4 + - - +
168A PRO* 3.5 8.1 - - + +
170A ALA* 1.3 75.5 - - - +
172A ALA* 1.3 63.5 + - - +
174A ARG* 3.1 6.1 + - - +
175A ILE* 3.0 40.4 + - + +
183A VAL* 5.9 1.8 - - + -
201A ASN 5.4 1.8 - - - +
202A VAL* 5.3 7.6 - - + -
205A ALA* 3.9 11.9 - - + -
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Residues in contact with ALA 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 PRO 2.9 18.4 + - - +
169A GLU* 4.0 6.1 - - - +
171A VAL* 1.3 72.8 - - - +
173A GLY* 1.3 52.9 + - - +
175A ILE* 3.0 10.0 + - - +
176A ILE* 2.8 40.2 + - - +
205A ALA* 3.6 29.1 - - + +
208A ASN* 4.1 19.3 - - + +
211A VAL* 4.0 9.9 - - + -
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Residues in contact with GLY 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 GLU 3.3 11.3 + - - -
170A ALA* 4.0 3.1 - - - -
171A VAL 3.3 0.8 - - - -
172A ALA* 1.3 78.2 - - - +
174A ARG* 1.3 62.7 + - - +
176A ILE* 3.2 10.4 + - - +
177A ASP* 3.0 27.0 + - - +
208A ASN* 5.7 0.2 - - - +
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Residues in contact with ARG 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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160A SER* 5.4 0.6 + - - +
161A VAL 5.9 0.2 - - - -
162A ILE* 3.9 40.1 - - + +
166A PHE* 3.1 38.1 - - - -
170A ALA* 3.2 38.1 + - - +
171A VAL 3.1 7.4 + - - +
173A GLY* 1.3 75.2 - - - +
175A ILE* 1.3 54.1 + - - +
178A SER* 2.7 36.4 + - - -
263A TYR* 3.4 54.5 + - + +
265A SER* 5.7 0.8 + - - -
271A PRO* 3.7 32.9 - - - +
531A GLU* 5.5 0.2 + - - -
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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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136A ALA* 4.3 19.5 - - + -
162A ILE* 4.6 1.8 - - + -
171A VAL* 3.0 37.4 + - + +
172A ALA* 3.0 11.2 + - - +
174A ARG* 1.3 77.5 - - - +
176A ILE* 1.3 58.0 + - - +
178A SER* 3.3 6.0 + - - -
179A SER* 2.9 26.3 + - - -
180A SER* 3.4 8.1 + - - +
183A VAL* 3.9 22.9 - - + -
202A VAL* 6.2 0.9 - - + -
205A ALA* 4.9 1.3 - - + -
206A LEU* 4.0 15.7 - - + -
211A VAL* 4.0 17.0 - - + -
213A SER* 3.9 7.4 + - - +
214A VAL* 3.7 23.1 - - + -
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Residues in contact with ILE 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 ALA 2.8 28.9 + - - +
173A GLY* 3.2 7.4 + - - +
175A ILE* 1.3 70.3 - - - +
177A ASP* 1.3 67.8 + - - +
178A SER 3.2 0.5 + - - -
179A SER* 3.3 15.1 + - - +
208A ASN* 4.0 17.0 - - - +
210A ASN* 3.6 33.7 - - + +
211A VAL* 3.8 25.4 - - + +
213A SER* 5.3 1.6 - - - -
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Residues in contact with ASP 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 GLY 3.0 16.3 + - - +
176A ILE* 1.3 79.4 - - - +
178A SER* 1.3 58.0 + - - +
179A SER* 4.8 1.7 + - - -
263A TYR* 2.4 41.2 + - + +
271A PRO 5.8 0.7 - - - +
272A LYS* 4.8 16.4 - - - +
273A GLY 4.8 1.6 + - - -
478A PHE* 3.3 31.6 - - - +
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Residues in contact with SER 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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134A VAL* 3.6 34.9 - - - +
160A SER* 5.1 2.3 - - - -
174A ARG 2.7 23.0 + - - -
175A ILE 3.3 2.1 + - - -
177A ASP* 1.3 78.0 - - - +
179A SER* 1.3 68.6 + - - +
180A SER* 2.6 26.0 + - - -
261A ILE* 5.6 2.2 - - - -
263A TYR* 3.5 18.4 - - - -
478A PHE* 3.8 16.2 - - - -
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Residues in contact with SER 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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134A VAL* 4.6 4.0 + - - +
175A ILE 2.9 6.7 + - - -
176A ILE 3.3 10.7 + - - -
177A ASP 4.8 1.2 + - - -
178A SER* 1.3 79.7 - - - +
180A SER* 1.3 66.1 + - - +
181A ARG* 3.4 13.5 + - - +
213A SER* 3.4 22.9 - - - -
478A PHE* 5.7 2.1 - - - -
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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