Contacts of the helix formed by residues 162 - 175 (chain A) in PDB entry 1GPU
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 GLU 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.5 24.5 - - + +
119A GLY* 4.3 0.2 - - - -
158A GLY 3.3 7.0 + - - +
159A CYS 3.4 8.0 + - - +
160A LEU 4.4 0.7 - - - +
161A GLN* 1.3 76.9 - - - +
163A GLY* 1.3 66.8 + - - +
164A ILE* 4.0 10.9 + - + -
165A SER* 3.0 24.3 + - - -
166A SER* 3.8 2.1 + - - -
1682A THD 3.1 10.2 - - - +
167B GLU* 3.7 12.3 - - - +
416B ILE* 3.1 34.4 - - + +
418B GLU* 2.5 29.9 + - - +
419B HIS 5.6 0.2 + - - -
448B TYR* 3.3 19.9 - - - -
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Residues in contact with GLY 163 (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 GLN 4.4 0.2 - - - -
162A GLU* 1.3 71.6 + - - +
164A ILE* 1.3 62.6 + - - +
166A SER* 3.0 19.8 + - - -
167A GLU* 3.1 9.9 + - - +
163B GLY* 3.5 33.0 - - - -
166B SER* 5.1 0.2 - - - -
167B GLU* 2.7 31.0 + - - +
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Residues in contact with ILE 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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118A LEU 4.3 2.9 - - - +
119A GLY* 3.5 28.0 - - - +
120A GLN* 3.7 11.0 - - - +
123A SER* 3.4 9.9 - - - +
162A GLU* 4.0 9.6 + - + -
163A GLY* 1.3 75.1 - - - +
165A SER* 1.3 59.9 + - - +
167A GLU* 3.3 12.6 + - - +
168A ALA* 3.0 26.2 + - - +
419A HIS* 3.3 60.5 + - + +
420A ALA* 3.8 11.4 - - - +
423A ALA* 3.6 21.8 - - + -
167B GLU* 4.7 0.2 + - - -
448B TYR* 4.9 0.9 - - + -
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLY* 4.5 2.9 - - - -
122A ILE* 3.7 22.9 - - - -
123A SER* 4.1 7.6 - - - -
159A CYS 2.6 31.2 + - - -
160A LEU* 3.7 12.1 + - - +
162A GLU 3.0 10.9 + - - -
164A ILE* 1.3 78.0 - - - +
166A SER* 1.3 60.1 + - - +
168A ALA* 4.0 1.3 - - - +
169A SER* 2.7 37.4 + - - -
206A ARG* 5.2 1.0 + - - -
207A TYR* 4.7 8.9 + - - -
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Residues in contact with SER 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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160A LEU 4.7 3.1 + - - -
162A GLU 4.7 2.8 + - - -
163A GLY* 3.0 11.1 + - - -
165A SER* 1.3 77.0 + - - +
167A GLU* 1.3 61.2 + - - +
169A SER* 3.8 0.4 - - - -
170A SER* 2.8 32.9 + - - -
206A ARG* 3.2 23.5 + - - +
210A TYR* 3.3 18.5 + - - -
163B GLY* 5.1 0.9 - - - -
166B SER* 3.7 30.6 - - - -
210B TYR* 4.7 0.5 + - - -
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Residues in contact with GLU 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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163A GLY 3.1 7.6 + - - +
164A ILE* 3.5 5.5 - - - +
166A SER* 1.3 80.4 - - - +
168A ALA* 1.3 63.7 + - - +
170A SER* 3.3 0.8 + - - -
171A LEU* 3.1 19.1 + - - +
417A ARG* 3.3 43.6 + - + +
419A HIS* 3.6 14.2 + - - +
420A ALA* 2.8 37.3 + - + +
448A TYR* 5.8 0.2 - - - -
161B GLN 3.4 12.6 - - - +
162B GLU* 3.7 8.9 - - - +
163B GLY* 2.8 35.6 + - - +
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Residues in contact with ALA 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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122A ILE* 5.0 1.3 - - + +
123A SER* 3.4 40.4 - - - +
126A VAL* 3.7 17.1 - - + +
164A ILE 3.0 6.4 + - - +
165A SER* 4.0 3.4 - - - +
167A GLU* 1.3 80.3 - - - +
169A SER* 1.3 58.7 + - - +
171A LEU* 3.5 2.4 + - - +
172A ALA* 2.8 28.9 + - - +
420A ALA* 3.6 11.2 - - + +
424A ILE* 4.7 8.1 - - + -
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 4.6 10.0 - - - +
126A VAL* 5.2 0.2 - - - -
165A SER 2.7 24.5 + - - -
168A ALA* 1.3 74.7 - - - +
170A SER* 1.3 65.4 - - - +
172A ALA* 4.1 3.4 - - - -
173A GLY 3.0 7.8 + - - -
207A TYR* 2.7 40.9 + - - -
210A TYR* 3.7 15.0 - - - +
212A TRP* 2.9 32.3 + - - +
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Residues in contact with SER 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 SER 2.8 19.0 + - - -
167A GLU* 3.6 4.9 - - - -
169A SER* 1.3 76.4 - - - +
171A LEU* 1.3 63.5 + - - +
173A GLY* 3.3 3.1 + - - -
174A HIS* 3.1 21.0 + - - +
210A TYR* 3.6 18.8 - - - +
417A ARG* 3.0 22.3 + - - -
199B PHE* 4.3 0.9 - - - -
200B ASP* 5.2 0.7 + - - +
201B GLU* 2.6 34.7 + - - +
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Residues in contact with LEU 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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126A VAL* 5.5 0.2 - - + -
130A MET* 5.0 0.9 - - - -
167A GLU 3.1 13.4 + - - +
168A ALA 3.9 3.8 - - - +
170A SER* 1.3 78.6 - - - +
172A ALA* 1.3 59.4 + - - +
174A HIS* 3.2 11.4 + - + +
175A LEU* 2.9 58.9 + - + +
412A ILE* 4.9 3.6 - - + -
413A ARG 3.7 20.4 - - - +
414A TYR* 3.8 28.0 - - + +
417A ARG* 3.8 23.2 - - + +
420A ALA* 5.8 0.4 - - + -
424A ILE* 3.6 28.5 - - + -
198B SER 4.3 5.4 - - - +
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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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126A VAL* 3.9 20.8 - - + +
168A ALA 2.8 18.8 + - - +
169A SER 3.7 5.2 - - - +
170A SER 3.3 0.2 - - - -
171A LEU* 1.3 76.0 - - - +
173A GLY* 1.3 64.4 + - - +
175A LEU* 3.3 2.0 + - - +
176A LYS 3.1 16.8 + - - -
177A LEU* 3.5 27.2 + - + +
180A LEU* 4.3 4.0 - - + -
212A TRP* 3.8 21.1 - - + -
241A PRO* 3.9 4.4 - - + +
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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 SER 3.0 13.5 + - - -
170A SER 3.7 1.1 - - - -
172A ALA* 1.3 74.7 - - - +
174A HIS* 1.3 64.7 + - - +
176A LYS* 3.1 19.4 + - - +
210A TYR 3.2 24.6 - - - +
211A GLY* 4.6 7.1 - - - +
212A TRP* 3.6 12.5 - - - +
241A PRO* 4.1 6.5 - - - -
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Residues in contact with HIS 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 SER 3.1 13.3 + - - +
171A LEU* 3.2 12.8 + - + +
173A GLY* 1.3 76.3 - - - +
175A LEU* 1.3 79.7 + - + +
176A LYS* 3.3 9.8 + - - +
210A TYR 3.9 1.6 + - - -
398A GLN* 2.7 25.5 + - - -
399A PRO* 3.4 15.0 - - + +
402A SER* 5.4 6.3 - - - -
413A ARG 5.6 0.2 - - - -
196B SER 3.1 24.4 + - - -
197B ILE* 3.1 16.7 + - - -
198B SER* 4.0 17.0 + - - +
200B ASP* 2.7 43.7 + - - +
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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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130A MET* 3.6 43.5 - - + -
171A LEU* 2.9 36.6 + - + +
172A ALA 3.8 4.3 - - - +
173A GLY 3.1 0.4 - - - -
174A HIS* 1.3 95.1 - - + +
176A LYS* 1.3 58.0 + - - +
177A LEU* 3.2 14.5 + - + +
397A PHE* 4.0 23.8 - - + +
398A GLN* 3.8 12.8 - - - +
399A PRO* 3.2 12.9 - - + +
407A TYR* 2.7 31.2 + - - -
412A ILE* 5.5 2.0 - - + -
413A ARG 6.1 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