Contacts of the helix formed by residues 355 - 371 (chain F) in PDB entry 2GL7
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 GLN 355 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164D ASP* 5.0 6.5 - - - +
356F LEU* 1.3 70.9 + - + +
357F GLU* 3.1 37.2 + - - -
358F HIS* 3.3 17.5 + - + +
359F ARG* 3.7 7.6 + - - +
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Residues in contact with LEU 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355F GLN* 1.3 82.1 - - + +
357F GLU* 1.3 80.3 + - + +
358F HIS 3.4 0.2 - - - -
359F ARG* 3.5 18.9 + - + +
360F GLU* 3.1 24.1 + - - +
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Residues in contact with GLU 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355F GLN* 3.1 33.2 + - - +
356F LEU* 1.3 93.9 - - + +
358F HIS* 1.3 65.5 + - + +
360F GLU* 3.5 5.8 + - - +
361F ARG* 3.3 36.2 + - - +
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Residues in contact with HIS 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ASP* 3.1 29.8 + - - -
163D GLU* 6.2 1.6 - - + -
164D ASP* 5.2 7.6 - - + +
355F GLN* 3.3 10.9 + - + +
357F GLU* 1.3 81.7 - - + +
359F ARG* 1.3 66.1 + - - +
361F ARG* 3.6 23.8 + - - +
362F SER* 3.1 40.3 + - - -
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Residues in contact with ARG 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ASP* 3.2 43.2 + - - +
166D VAL* 3.5 30.3 - - - +
167D VAL* 4.4 9.4 - - - +
355F GLN 3.7 3.2 + - - +
356F LEU* 3.5 23.7 + - + +
357F GLU 3.4 0.2 - - - -
358F HIS* 1.3 79.5 - - - +
360F GLU* 1.3 60.4 + - + +
362F SER* 3.8 0.9 - - - -
363F LEU* 2.9 54.4 + - + +
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Residues in contact with GLU 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356F LEU 3.1 16.6 + - - +
357F GLU* 3.8 6.3 - - - +
358F HIS 3.3 0.2 - - - -
359F ARG* 1.3 77.4 - - + +
361F ARG* 1.3 66.7 + - - +
363F LEU* 4.0 4.0 - - - +
364F GLN* 3.1 26.3 + - - +
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Residues in contact with ARG 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357F GLU* 3.3 27.4 + - - +
358F HIS* 3.6 29.9 + - - +
360F GLU* 1.3 79.0 - - - +
362F SER* 1.3 59.5 + - - +
364F GLN* 3.8 4.7 - - - +
365F THR* 2.9 29.8 + - - +
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Residues in contact with SER 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D LEU* 3.7 24.6 - - - +
162D ASP* 4.7 0.8 + - - -
167D VAL* 4.0 15.5 - - - -
358F HIS* 3.1 41.0 + - - -
359F ARG 4.0 2.2 - - - -
361F ARG* 1.3 74.2 + - - +
363F LEU* 1.3 66.3 + - - +
365F THR* 3.4 8.0 + - - -
366F LEU* 3.3 26.0 + - - +
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Residues in contact with LEU 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D VAL* 4.5 17.5 - - + +
167D VAL* 4.6 13.9 - - + +
170D LYS* 4.8 12.3 - - + -
359F ARG* 2.9 39.2 + - - +
360F GLU* 4.0 5.2 - - - +
362F SER* 1.3 75.6 - - - +
364F GLN* 1.3 61.4 + - - +
366F LEU* 3.3 11.6 + - + +
367F ARG* 3.1 21.1 + - + +
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Residues in contact with GLN 364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360F GLU 3.1 18.5 + - - +
361F ARG* 3.8 5.6 - - - +
363F LEU* 1.3 76.3 - - - +
365F THR* 1.3 58.7 + - - +
367F ARG* 3.3 13.3 + - - +
368F ASP* 2.8 55.8 + - - +
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Residues in contact with THR 365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D GLU* 4.0 25.8 + - + +
159D LEU* 4.9 3.4 - - + -
361F ARG* 2.9 18.2 + - - +
362F SER* 3.6 11.3 - - - -
363F LEU 3.3 0.4 - - - -
364F GLN* 1.3 78.3 - - - +
366F LEU* 1.3 50.2 - - - +
368F ASP* 3.5 8.7 - - + +
369F ILE* 1.9 58.3 + - + +
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Residues in contact with LEU 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 4.3 8.1 - - + -
159D LEU* 3.7 24.5 - - + -
167D VAL* 3.8 24.0 - - + +
170D LYS* 3.8 26.9 - - + -
171D ALA* 4.0 15.7 - - + +
174D MET* 3.4 45.0 - - + +
362F SER 3.3 14.3 + - - +
363F LEU* 3.3 14.9 + - + +
364F GLN 3.2 0.6 - - - -
365F THR* 1.3 76.7 - - - +
367F ARG* 1.3 63.5 + - - +
369F ILE* 3.5 9.2 + - + +
370F GLN* 3.6 7.4 + - - +
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Residues in contact with ARG 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363F LEU* 3.1 16.0 + - + +
364F GLN* 3.3 22.2 + - - +
366F LEU* 1.3 76.8 - - - +
368F ASP* 1.3 63.1 + - - +
369F ILE 3.5 0.2 + - - -
370F GLN* 3.7 15.2 + - - +
371F ARG* 4.4 2.9 + - - +
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Residues in contact with ASP 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364F GLN* 2.8 50.7 + - - +
365F THR* 3.5 11.6 - - + +
367F ARG* 1.3 77.8 - - - +
369F ILE* 1.3 58.4 + - + +
371F ARG* 3.3 27.6 + - - +
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Residues in contact with ILE 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ALA* 4.3 29.6 - - + +
155D GLU* 4.2 15.9 - - + -
156D LEU* 4.2 20.4 - - + -
159D LEU* 4.3 4.5 - - + -
174D MET* 4.8 6.4 - - - +
365F THR* 1.9 58.6 - - + +
366F LEU* 3.5 11.7 - - + +
367F ARG 3.3 0.4 - - - -
368F ASP* 1.3 72.5 - - + +
370F GLN* 1.3 65.2 + - - +
371F ARG 3.3 7.1 - - - +
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Residues in contact with GLN 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D MET* 4.7 10.3 - - + -
366F LEU 3.6 9.9 + - - +
367F ARG* 3.8 12.3 - - - +
368F ASP 3.3 0.8 - - - -
369F ILE* 1.3 78.6 - - - +
371F ARG* 1.3 63.2 + - - +
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Residues in contact with ARG 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367F ARG 4.4 2.6 + - - +
368F ASP* 3.3 18.8 + - - +
369F ILE* 4.0 6.8 - - - +
370F GLN* 1.3 84.3 - - - +
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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