Contacts of the helix formed by residues 361 - 368 (chain D) 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 GLY 361 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325D VAL* 3.9 2.5 - - - +
329D ARG* 4.5 6.4 + - - -
358D VAL 3.3 5.0 + - - -
359D GLU 3.1 6.4 + - - -
360D ALA* 1.3 81.6 - - - +
362D GLY* 1.3 64.1 + - - +
363D MET 3.3 3.3 + - - -
364D GLN* 3.5 20.4 - - - +
365D ALA* 3.2 24.8 + - - +
395D GLN* 4.6 2.9 - - - -
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Residues in contact with GLY 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D VAL* 3.6 18.6 - - - -
357D ILE* 2.9 30.1 + - - -
358D VAL 3.9 1.6 + - - -
360D ALA 3.4 1.0 - - - -
361D GLY* 1.3 78.4 - - - +
363D MET* 1.3 61.6 + - - +
365D ALA* 3.6 1.0 + - - +
366D LEU* 3.2 35.5 + - - +
388D LEU* 4.9 0.4 - - - -
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Residues in contact with MET 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D VAL* 4.3 13.9 - - + +
361D GLY 3.3 1.0 - - - -
362D GLY* 1.3 73.8 - - - +
364D GLN* 1.3 72.4 + - - +
367D GLY* 3.1 18.7 + - - -
385D LEU* 3.4 49.1 - - + +
388D LEU* 3.4 32.5 - - - -
389D SER* 4.1 4.9 - - - -
392D ALA* 3.7 32.8 - - + -
395D GLN* 5.1 1.8 - - + -
398D MET* 4.3 15.3 - - + -
401D LEU* 3.9 7.7 - - + +
423D ILE* 5.0 1.1 - - + -
427D LEU* 4.0 23.1 - - + -
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Residues in contact with GLN 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D GLY* 3.5 25.6 - - - +
363D MET* 1.3 77.4 + - - +
365D ALA* 1.3 64.9 + - - +
367D GLY* 3.2 11.0 + - - +
368D LEU* 3.3 20.4 + - + +
395D GLN* 3.1 23.8 + - - +
396D GLU 2.6 27.5 + - - -
397D GLY* 3.3 22.8 + - - +
398D MET* 4.1 15.0 - - - -
401D LEU* 5.2 7.0 - - + -
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Residues in contact with ALA 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D VAL* 4.1 14.6 - - + +
328D MET* 4.3 10.5 - - + -
329D ARG* 3.6 27.7 - - + +
361D GLY 3.2 18.3 + - - +
362D GLY* 3.8 4.5 - - - +
363D MET 3.3 0.2 - - - -
364D GLN* 1.3 74.7 - - - +
366D LEU* 1.3 66.2 + - + +
368D LEU* 3.2 31.2 + - - +
369D HIS* 3.4 10.4 + - - -
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Residues in contact with LEU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D MET* 4.2 12.6 - - + -
341D SER* 5.1 4.9 - - - -
344D LEU* 4.1 25.4 - - + -
357D ILE* 5.5 0.4 - - + -
362D GLY* 3.2 19.1 + - - +
363D MET 3.9 3.8 - - - +
365D ALA* 1.3 77.9 - - + +
367D GLY* 1.3 61.3 + - - +
369D HIS* 3.3 12.4 + - - -
370D LEU* 3.6 15.8 - - - +
381D CYS* 3.8 34.4 - - + +
384D THR* 3.5 33.4 - - + -
385D LEU* 3.9 20.4 - - + -
388D LEU* 3.8 14.6 - - + -
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Residues in contact with GLY 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D MET 3.1 14.5 + - - -
364D GLN* 3.2 7.2 + - - -
365D ALA 3.1 0.8 - - - -
366D LEU* 1.3 76.4 - - - +
368D LEU* 1.3 63.3 + - - +
369D HIS 3.3 1.0 + - - -
370D LEU* 3.5 30.7 + - - +
385D LEU* 4.6 0.4 - - - +
401D LEU* 4.1 14.2 - - - -
404D THR* 4.9 6.9 + - - +
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Residues in contact with LEU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D MET 4.6 1.6 - - - +
329D ARG* 4.4 26.9 - - + +
364D GLN* 3.3 12.2 + - + +
365D ALA* 3.2 28.6 + - - +
367D GLY* 1.3 78.7 - - - +
369D HIS* 1.3 70.0 + - + +
370D LEU 3.5 0.6 + - - -
371D THR* 4.9 5.5 + - - -
372D ASP 5.5 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