Contacts of the helix formed by residues 162 - 175 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A GLU* 3.7 12.4 - - - +
416A ILE* 3.2 27.9 - - + +
418A GLU* 2.5 29.0 + - - +
419A HIS 5.6 0.2 + - - -
448A TYR* 3.4 19.9 - - - -
118B LEU* 3.5 24.5 - - + +
119B GLY* 4.3 0.9 - - - -
158B GLY 3.4 6.2 + - - +
159B CYS 3.4 8.8 + - - +
160B LEU 4.4 0.7 - - - +
161B GLN* 1.3 77.1 - - - +
163B GLY* 1.3 68.2 + - - +
164B ILE* 3.0 12.3 + - + -
165B SER* 2.9 24.6 + - - -
166B SER* 3.8 2.0 + - - -
1682B THD 3.1 14.7 - - - +
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Residues in contact with GLY 163 (chain B).
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* 3.5 33.9 - - - -
166A SER* 5.1 0.7 - - - -
167A GLU* 2.8 29.8 + - - +
162B GLU* 1.3 72.0 + - - +
164B ILE* 1.3 62.3 + - - +
166B SER* 3.0 20.3 + - - -
167B GLU* 3.1 10.2 + - - +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A TYR* 4.9 0.7 - - + -
118B LEU 4.3 2.9 - - - +
119B GLY* 3.4 28.9 - - - +
120B GLN* 3.7 11.9 - - - +
123B SER* 3.5 14.4 - - - +
162B GLU* 3.0 10.2 + - + -
163B GLY* 1.3 75.8 - - - +
165B SER* 1.3 60.6 + - - +
167B GLU* 3.3 11.2 + - - +
168B ALA* 3.0 27.0 + - - +
419B HIS* 3.4 57.9 + - + +
420B ALA* 3.8 11.9 - - - +
423B ALA* 3.7 15.5 - - + -
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Residues in contact with SER 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLY* 4.5 2.5 - - - -
122B ILE* 3.7 23.6 - - - -
123B SER* 4.1 7.9 - - - -
155B LEU* 5.6 1.1 - - - -
159B CYS 2.6 31.0 + - - -
160B LEU* 3.8 10.2 + - - -
162B GLU 2.9 11.4 + - - -
164B ILE* 1.3 77.0 - - - +
166B SER* 1.3 60.0 + - - +
168B ALA* 4.0 1.2 - - - +
169B SER* 2.7 38.0 + - - -
206B ARG* 5.4 0.7 + - - -
207B TYR* 4.8 9.2 + - - -
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Residues in contact with SER 166 (chain B).
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* 5.1 1.1 - - - -
166A SER* 3.7 29.9 - - - -
210A TYR* 4.7 0.5 + - - -
160B LEU 4.7 3.3 + - - -
162B GLU 4.7 2.6 + - - -
163B GLY* 3.0 11.5 + - - -
165B SER* 1.3 78.5 + - - +
167B GLU* 1.3 61.5 + - - +
170B SER* 2.9 32.8 + - - -
206B ARG* 3.2 24.1 + - - +
210B TYR* 3.3 18.7 + - - -
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Residues in contact with GLU 167 (chain B).
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 3.4 12.8 - - - +
162A GLU* 3.7 8.0 - - - +
163A GLY* 2.7 37.5 + - - +
164A ILE 4.7 0.2 + - - -
163B GLY 3.1 11.6 + - - +
164B ILE* 3.5 4.5 - - - +
166B SER* 1.3 78.3 - - - +
168B ALA* 1.3 62.0 + - - +
170B SER* 4.6 0.7 - - - -
171B LEU* 3.1 19.4 + - - +
417B ARG* 3.3 44.9 + - + +
419B HIS* 3.5 13.7 + - - +
420B ALA* 2.9 36.4 + - + +
448B TYR* 5.8 0.3 - - - -
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ILE* 5.1 1.1 - - + -
123B SER* 3.4 41.1 - - - +
126B VAL* 3.8 14.0 - - + +
164B ILE 3.0 5.8 + - - +
165B SER* 4.0 3.8 - - - +
167B GLU* 1.3 80.0 - - - +
169B SER* 1.3 58.4 + - - +
171B LEU* 3.6 2.4 + - - +
172B ALA* 2.9 28.9 + - - +
420B ALA* 3.6 10.5 - - + +
424B ILE* 4.6 9.6 - - + -
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Residues in contact with SER 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 4.5 10.4 - - - +
126B VAL* 5.2 0.4 - - - -
165B SER 2.7 21.0 + - - -
168B ALA* 1.3 73.2 - - - +
170B SER* 1.3 65.5 + - - +
172B ALA* 4.1 3.4 - - - -
173B GLY 3.0 8.5 + - - -
207B TYR* 2.7 43.0 + - - -
210B TYR* 3.7 15.2 - - - +
212B TRP* 2.8 32.3 + - - +
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PHE* 4.2 1.2 - - - -
201A GLU* 2.7 33.2 + - - +
166B SER 2.9 19.2 + - - -
167B GLU* 3.6 4.3 - - - -
169B SER* 1.3 75.3 - - - +
171B LEU* 1.3 64.0 + - - +
173B GLY* 3.3 2.6 + - - -
174B HIS* 3.1 21.1 + - - +
210B TYR* 3.6 19.6 - - - +
417B ARG* 3.0 23.6 + - - -
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A SER 4.3 6.3 - - - +
126B VAL* 5.5 0.2 - - + -
130B MET* 5.0 0.9 - - - -
167B GLU 3.1 14.0 + - - +
168B ALA* 3.8 4.7 - - - +
170B SER* 1.3 77.9 - - - +
172B ALA* 1.3 59.5 + - - +
174B HIS* 3.2 12.3 + - + +
175B LEU* 2.9 58.7 + - + +
412B ILE* 4.9 3.6 - - + -
413B ARG 3.8 15.9 - - - +
414B TYR* 3.8 31.2 - - + +
417B ARG* 3.8 25.3 - - + +
420B ALA* 5.9 0.9 - - + -
424B ILE* 3.7 25.8 - - + -
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL* 3.9 19.9 - - + +
168B ALA 2.9 18.7 + - - +
169B SER 3.7 4.7 - - - +
170B SER 3.3 0.2 - - - -
171B LEU* 1.3 76.0 - - - +
173B GLY* 1.3 63.0 + - - +
175B LEU* 3.3 2.5 + - - +
176B LYS* 3.1 17.3 + - - -
177B LEU* 3.5 27.4 + - + +
180B LEU* 4.3 3.6 - - + -
212B TRP* 3.8 21.5 - - + -
241B PRO* 3.9 4.5 - - + +
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Residues in contact with GLY 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B SER 3.0 13.2 + - - -
170B SER 3.7 0.9 - - - -
171B LEU 3.2 0.2 - - - -
172B ALA* 1.3 74.9 - - - +
174B HIS* 1.3 64.6 + - - +
176B LYS* 3.1 20.1 + - - +
210B TYR 3.2 25.0 - - - +
211B GLY* 4.6 7.2 - - - +
212B TRP* 3.6 12.1 - - - +
241B PRO* 4.1 6.5 - - - -
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Residues in contact with HIS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A SER 3.1 24.3 + - - -
197A ILE* 3.1 15.5 + - - -
198A SER* 4.0 16.5 + - - +
200A ASP* 2.8 41.8 + - - +
170B SER 3.1 13.3 + - - +
171B LEU* 3.2 14.1 + - + +
173B GLY* 1.3 75.6 - - - +
175B LEU* 1.3 74.9 + - + +
176B LYS* 3.2 10.0 + - - +
210B TYR 3.9 1.4 + - - -
398B GLN* 2.7 30.6 + - - -
399B PRO* 3.4 14.9 - - + +
402B SER* 5.4 6.1 - - - -
413B ARG 5.6 0.4 - - - -
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B MET* 3.7 43.7 - - + -
171B LEU* 2.9 35.1 + - + +
172B ALA* 3.7 4.9 - - - +
173B GLY 3.2 0.2 - - - -
174B HIS* 1.3 94.9 - - + +
176B LYS* 1.3 56.7 + - - +
177B LEU* 3.2 14.3 + - + +
397B PHE* 4.0 24.2 - - + +
398B GLN* 3.8 13.0 - - - +
399B PRO* 3.2 12.3 - - + +
407B TYR* 2.7 31.4 + - - -
412B ILE* 5.4 2.7 - - + -
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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