Contacts of the helix formed by residues 360 - 373 (chain B) in PDB entry 2GQ3
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 360 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B PHE 5.4 0.2 - - - +
278B ALA* 3.9 13.0 - - - +
284B LYS* 2.7 38.7 + - + +
341B VAL* 3.6 24.2 - - + +
345B MET* 3.0 36.3 + - - +
346B THR 4.4 1.4 - - - +
347B ASN* 3.8 27.5 + - + -
358B VAL 3.3 1.4 + - - -
359B PHE* 1.3 71.0 - - - +
361B GLY* 1.3 60.4 + - - +
363B MET* 3.1 11.5 + - + +
364B ASP* 2.8 28.9 + - - +
715B HIS* 4.1 11.3 - - - -
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Residues in contact with GLY 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASN* 5.9 0.9 - - - -
340B ASN* 4.6 0.5 - - - +
341B VAL* 3.6 20.0 - - - +
342B GLY 4.0 7.1 + - - -
343B HIS* 5.6 1.9 - - - +
345B MET 4.4 1.6 + - - -
359B PHE* 3.4 2.0 - - - +
360B GLU* 1.3 76.7 - - - +
362B ILE* 1.3 61.2 + - - +
364B ASP* 3.5 4.3 + - - +
365B ALA* 3.1 23.0 + - - +
397B LYS* 3.7 26.2 + - - -
412B LEU* 4.0 1.9 - - - +
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Residues in contact with ILE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.5 7.4 - - + -
43B VAL* 4.1 26.7 - - + -
46B LEU* 4.3 8.5 - - + -
47B THR* 4.0 32.1 - - - +
50B ASN* 3.8 23.7 + - - +
358B VAL* 5.4 0.4 - - + -
359B PHE* 3.7 19.8 + - + +
360B GLU 3.3 0.4 - - - -
361B GLY* 1.3 77.5 - - - +
363B MET* 1.3 59.4 + - - +
365B ALA* 3.5 2.8 + - - +
366B LEU* 3.3 29.0 + - + +
408B PHE* 4.4 6.5 - - + -
412B LEU* 3.7 32.4 - - + +
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Residues in contact with MET 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.9 0.2 - - - -
43B VAL* 5.5 0.9 - - + -
284B LYS* 5.5 2.5 - - + -
288B TYR* 4.1 5.6 - - - +
347B ASN* 3.5 38.4 - - + +
349B ALA* 4.3 6.7 - - + -
350B ILE* 3.6 40.2 - - + -
358B VAL* 3.5 33.4 - - + +
359B PHE 3.4 7.3 + - - +
360B GLU* 3.1 14.8 + - + +
362B ILE* 1.3 72.7 - - + +
364B ASP* 1.3 62.3 + - - +
365B ALA 3.2 0.3 + - - -
366B LEU* 3.3 10.2 + - + +
367B PHE* 2.8 53.9 + - + -
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Residues in contact with ASP 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 4.1 5.2 - - - +
284B LYS* 3.2 28.9 + - - +
288B TYR* 2.8 25.5 + - - -
340B ASN* 3.4 21.0 - - + -
341B VAL* 3.1 26.3 + - - +
360B GLU 2.8 19.4 + - - +
361B GLY* 3.6 6.5 - - - +
363B MET* 1.3 76.8 - - - +
365B ALA* 1.3 51.9 + - - +
368B THR* 2.6 48.1 + - + -
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Residues in contact with ALA 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASN* 3.5 13.0 + - - +
361B GLY 3.1 16.7 + - - +
362B ILE 3.8 4.7 - - - +
363B MET 3.2 0.2 - - - -
364B ASP* 1.3 74.0 - - - +
366B LEU* 1.3 58.9 + - - +
368B THR* 4.2 0.7 - - - -
369B GLY* 2.8 30.8 + - - -
412B LEU* 3.9 20.2 - - + -
413B PHE* 4.1 14.8 - - + -
416B VAL* 3.7 19.4 - - + +
427B MET* 3.9 6.3 - - + +
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 4.4 8.0 - - + -
39B VAL* 3.8 47.8 - - + +
42B VAL* 4.7 7.9 - - + -
43B VAL* 4.6 5.2 - - + -
362B ILE* 3.3 29.3 + - + +
363B MET* 3.4 13.0 - - + +
365B ALA* 1.3 79.1 - - - +
367B PHE* 1.3 71.1 + - + +
369B GLY 3.9 0.2 - - - -
370B LEU* 3.0 25.8 + - - +
416B VAL* 3.8 27.4 - - + +
419B VAL* 4.5 16.8 - - + -
420B LEU* 4.3 7.0 - - + +
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Residues in contact with PHE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.9 22.2 - - + -
19B PHE* 6.0 1.1 - - + -
20B VAL* 4.1 16.2 - - + -
35B PHE* 3.5 36.3 - + - -
36B TRP* 4.2 12.8 - + - -
39B VAL* 4.5 7.2 - - + -
288B TYR* 3.5 38.6 - + + -
350B ILE* 3.9 18.8 - - + -
363B MET* 2.8 48.8 + - + +
366B LEU* 1.3 73.3 - - + +
368B THR* 1.3 67.5 + - - +
369B GLY 3.1 1.3 - - - -
370B LEU* 3.1 7.1 + - + +
371B ILE* 2.9 31.0 + - + +
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Residues in contact with THR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PHE* 3.9 25.6 - - + -
288B TYR* 3.9 21.3 - - + -
291B TRP* 3.1 26.5 + - + +
338B VAL* 4.0 9.6 - - + +
340B ASN* 3.0 30.8 + - - +
364B ASP* 2.6 32.2 + - + +
365B ALA* 4.0 1.4 + - - -
367B PHE* 1.3 71.4 - - - +
369B GLY* 1.3 60.0 + - - -
371B ILE* 4.9 0.4 - - - -
372B ALA* 3.1 22.2 + - - +
393B ILE* 5.7 0.2 - - - -
395B ILE* 4.3 4.3 - - - +
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Residues in contact with GLY 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B ALA 2.8 20.7 + - - -
368B THR* 1.3 74.3 + - - +
370B LEU* 1.3 67.1 + - - +
372B ALA* 3.4 17.4 + - - +
373B ILE* 3.6 6.4 + - - +
393B ILE* 3.8 10.3 - - - +
395B ILE* 5.1 0.4 - - - -
420B LEU* 3.3 19.8 - - - +
427B MET* 4.4 12.8 - - - -
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.9 22.0 - - + -
24B ALA* 3.7 28.7 - - + +
25B LEU* 3.9 22.0 - - + +
28B THR* 3.7 30.8 - - + +
30B ILE* 4.5 2.0 - - + -
35B PHE* 4.1 12.1 - - + -
366B LEU 3.0 16.4 + - - +
367B PHE* 3.1 12.3 + - + +
369B GLY* 1.3 74.0 - - - +
371B ILE* 1.3 64.4 + - - +
373B ILE* 3.0 26.1 + - + +
374B HIS 4.4 0.2 + - - -
420B LEU* 3.5 24.3 - - + +
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 4.0 4.7 - - + -
24B ALA* 4.4 16.4 - - + -
288B TYR* 3.1 47.3 - - + +
291B TRP* 3.5 26.9 - - + -
292B LEU* 3.1 40.6 - - + +
295B ASN* 3.5 10.3 - - - +
367B PHE* 2.9 21.3 + - + +
370B LEU* 1.3 74.5 - - + +
372B ALA* 1.3 61.5 + - - +
374B HIS* 3.2 26.3 + - - -
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TRP* 4.3 12.3 - - + +
295B ASN* 3.9 13.4 - - - +
368B THR 3.1 19.7 + - - +
369B GLY 3.4 7.4 - - - +
370B LEU 3.1 0.4 - - - -
371B ILE* 1.3 74.2 - - - +
373B ILE* 1.3 65.0 + - - +
374B HIS 3.3 0.2 - - - -
375B GLY* 3.0 14.1 + - - -
376B LEU* 3.5 13.3 + - - +
393B ILE* 3.6 33.0 - - + -
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Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY 5.2 1.3 - - - +
28B THR* 4.1 40.6 - - + +
30B ILE* 4.5 8.1 - - + -
369B GLY 3.6 8.0 + - - +
370B LEU* 3.0 19.9 + - + +
372B ALA* 1.3 78.3 - - - +
374B HIS* 1.3 62.2 + - - +
376B LEU* 3.0 26.5 + - + +
377B LYS* 3.3 27.1 - - + +
382B ASN* 5.4 0.2 - - - +
393B ILE* 4.8 0.2 - - + -
420B LEU* 4.2 26.9 - - + +
422B LEU* 4.3 22.0 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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