Contacts of the helix formed by residues 168 - 184 (chain A) in PDB entry 1PHP
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 GLY 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A THR* 5.3 0.4 - - - -
6A ILE* 4.5 4.9 - - - -
43A THR* 3.9 5.8 - - - -
142A VAL* 3.7 14.6 - - - +
143A ASN 3.2 12.5 + - - -
144A ASP* 3.1 22.7 - - - +
167A ALA* 1.3 76.8 - - - +
169A PHE* 1.3 61.1 + - - -
172A GLU* 3.0 27.9 + - - +
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Residues in contact with PHE 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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5A THR* 4.9 2.2 - - - -
6A ILE* 3.7 17.2 - - + +
7A ARG* 3.5 48.7 - - + -
42A PRO* 3.8 33.7 - - + -
43A THR* 3.0 15.0 + - - +
46A TYR* 3.7 43.3 - + + -
168A GLY* 1.3 71.4 - - - -
170A LEU* 1.3 64.7 + - - +
172A GLU* 3.8 9.3 - - - +
173A LYS* 3.1 21.8 + - - +
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Residues in contact with LEU 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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21A ASP* 6.5 0.9 - - + -
36A ARG 5.6 0.7 - - - +
39A ALA* 3.6 44.4 - - + +
40A ALA* 4.5 3.4 - - + +
43A THR* 4.2 0.2 + - - -
144A ASP* 2.9 33.8 + - - +
146A PHE* 5.6 1.1 - - + +
169A PHE* 1.3 72.5 - - - +
171A MET* 1.3 66.8 + - - +
173A LYS* 3.1 27.5 + - - +
174A GLU* 3.0 29.6 + - + +
371A THR* 4.4 29.4 - - + +
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Residues in contact with MET 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 ASN* 3.3 59.7 - - + +
144A ASP* 3.0 12.4 + - - +
145A ALA 4.0 0.9 - - - -
146A PHE* 3.8 49.3 - - - +
149A ALA* 4.1 9.2 - - + -
167A ALA* 3.7 15.0 - - + -
168A GLY 3.8 2.9 - - - +
170A LEU* 1.3 76.1 - - - +
172A GLU* 1.4 57.8 + - - +
174A GLU* 3.2 3.1 + - - +
175A LEU* 2.9 50.0 + - + +
387A GLY 5.2 0.7 - - - +
388A VAL* 4.4 7.0 - - + -
391A LEU* 4.1 9.0 - - + -
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Residues in contact with GLU 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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5A THR* 3.7 22.0 - - + +
7A ARG* 2.6 42.4 + - - -
167A ALA* 4.7 4.7 - - + -
168A GLY 3.0 18.3 + - - +
169A PHE* 3.8 13.7 - - - +
170A LEU 3.2 0.2 - - - -
171A MET* 1.4 76.8 - - - +
173A LYS* 1.3 62.9 + - - +
175A LEU* 3.5 6.1 + - - +
176A GLU* 3.0 37.0 + - + +
394A LYS* 5.0 4.0 + - - +
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Residues in contact with LYS 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 PHE 3.1 13.7 + - - +
170A LEU* 3.1 29.1 + - - +
172A GLU* 1.3 77.1 - - - +
174A GLU* 1.3 64.0 + - - +
176A GLU* 3.3 4.0 + - - +
177A VAL* 3.1 32.6 + - + +
368A HIS* 3.9 28.5 - - + +
369A ILE 5.9 0.7 - - - -
371A THR* 6.2 1.9 - - - +
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Residues in contact with GLU 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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146A PHE* 3.7 39.0 - - + -
170A LEU* 3.0 22.5 + - + +
171A MET 3.2 5.6 + - - +
173A LYS* 1.3 76.8 - - + +
175A LEU* 1.3 63.7 + - - +
178A LEU* 3.1 37.5 + - - +
368A HIS* 2.9 28.3 + - + -
370A SER* 2.7 24.6 + - - -
371A THR* 2.8 40.2 + - - +
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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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1A MET* 3.5 22.9 + - - +
3A LYS* 4.2 22.7 - - + -
146A PHE* 4.1 16.4 - - + -
167A ALA* 5.2 1.6 - - + -
171A MET* 2.9 39.4 + - + +
172A GLU* 4.0 6.3 - - - +
174A GLU* 1.3 77.2 - - - +
176A GLU* 1.3 57.5 + - - +
179A GLY* 2.9 28.6 + - - +
379A PHE* 4.2 15.1 - - + -
388A VAL* 3.8 40.4 - - + -
391A LEU* 4.7 3.1 - - + -
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Residues in contact with GLU 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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1A MET* 3.3 40.5 - - - +
172A GLU* 3.0 33.0 + - + +
173A LYS* 3.8 5.2 - - - +
174A GLU 3.3 0.2 - - - -
175A LEU* 1.3 76.3 - - - +
177A VAL* 1.3 63.1 + - + +
180A LYS* 3.1 30.3 + - - +
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Residues in contact with VAL 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 LYS* 3.1 24.2 + - + +
176A GLU* 1.3 82.7 - - + +
178A LEU* 1.3 61.2 + - - +
180A LYS* 3.8 4.3 - - - +
181A ALA* 3.1 25.8 + - - +
345A TYR* 3.8 25.6 - - + +
347A VAL* 4.0 18.6 - - + -
368A HIS* 3.8 44.4 - - + +
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Residues in contact with LEU 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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146A PHE* 3.7 31.9 - - + -
174A GLU* 3.1 30.6 + - - +
177A VAL* 1.3 71.2 - - - +
179A GLY* 1.3 68.0 + - - +
181A ALA* 3.2 7.1 + - + +
182A LEU* 3.1 27.0 + - - +
347A VAL* 3.9 28.0 - - + -
368A HIS* 4.4 9.9 - - + +
370A SER* 4.1 7.9 - - - +
376A SER* 4.3 12.8 - - - +
379A PHE* 3.5 24.2 - - + -
380A MET* 4.8 15.9 - - + -
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Residues in contact with GLY 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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1A MET* 4.2 9.0 - - - -
175A LEU 2.9 22.2 + - - -
178A LEU* 1.3 77.3 - - - +
180A LYS* 1.3 55.2 + - - +
182A LEU* 3.3 4.4 + - - +
183A SER* 2.9 34.2 + - - -
379A PHE* 3.8 15.3 - - - -
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Residues in contact with LYS 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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1A MET* 3.9 14.2 - - + -
176A GLU 3.1 20.6 + - - +
177A VAL* 3.8 4.5 - - - +
179A GLY* 1.3 70.7 - - - +
181A ALA* 1.3 62.1 + - - +
183A SER* 3.9 6.3 - - - -
184A ASN* 2.8 67.8 + - + +
185A PRO* 3.9 1.1 - - - +
186A ASP* 3.2 35.9 + - - +
312A LEU* 6.2 0.9 - - - -
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Residues in contact with ALA 181 (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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177A VAL 3.1 15.6 + - - +
178A LEU* 3.2 11.4 + - + +
180A LYS* 1.3 78.7 - - - +
182A LEU* 1.3 65.0 - - + +
185A PRO* 3.5 19.1 - - - +
189A PHE* 3.5 13.0 - - + -
211A LYS* 5.5 0.2 - - - +
312A LEU* 4.1 26.5 - - + -
314A VAL* 4.2 18.8 - - + -
347A VAL* 5.2 4.7 - - + -
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Residues in contact with LEU 182 (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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178A LEU* 3.1 10.4 + - + +
179A GLY* 3.8 4.7 - - - +
181A ALA* 1.3 84.2 - - + +
183A SER* 1.3 60.8 + - - +
185A PRO* 4.3 2.6 - - - +
189A PHE* 5.5 0.9 - - + -
207A ASN* 4.2 17.9 - - - +
208A LEU* 4.4 18.2 - - + -
211A LYS* 3.3 38.4 + - + +
379A PHE* 3.4 48.9 - - + +
380A MET* 4.2 16.8 - - + +
382A GLY* 5.2 4.0 - - - -
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Residues in contact with SER 183 (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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1A MET* 3.6 20.2 - - - +
179A GLY* 2.9 20.2 + - - -
182A LEU* 1.3 80.4 - - - +
184A ASN* 1.3 66.2 + - - +
185A PRO* 3.7 3.5 - - - +
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Residues in contact with ASN 184 (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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1A MET* 5.7 2.2 - - + -
180A LYS* 2.8 49.4 + - + +
183A SER* 1.3 83.2 + - - +
185A PRO* 1.3 66.0 - - - +
186A ASP* 4.9 0.2 - - - +
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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