Contacts of the helix formed by residues 402 - 421 (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 GLY 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B HIS* 1.3 78.7 + - - +
403B PRO* 1.4 73.4 - - - +
404B ALA 3.4 1.1 - - - -
405B GLU* 3.3 8.3 + - - +
406B VAL* 3.5 13.0 + - - +
437B ARG* 3.2 26.6 + - - -
438B THR* 3.0 12.4 + - - +
445B CYS* 3.5 9.4 - - - -
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Residues in contact with PRO 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.7 30.3 - - + -
402B GLY* 1.4 80.0 - - - +
404B ALA* 1.3 67.8 + - - +
405B GLU 3.1 1.6 - - - -
406B VAL* 3.1 4.3 + - + +
407B ALA* 3.0 23.4 + - - +
437B ARG* 5.7 1.6 - - + +
441B ASN* 4.0 13.7 - - + +
444B ALA* 3.7 45.1 - - + +
445B CYS* 3.5 10.3 - - - -
448B ALA* 3.8 5.7 - - + +
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.0 20.8 - - + +
92B LEU* 5.6 1.9 - - + +
401B HIS 5.7 0.4 - - - +
402B GLY 3.4 1.0 - - - -
403B PRO* 1.3 82.4 - - - +
405B GLU* 1.3 58.4 + - + +
407B ALA* 3.4 8.8 + - - +
408B PHE* 3.1 26.7 + - - +
437B ARG* 6.0 4.2 - - - +
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Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.0 35.2 - - + +
57B ARG* 2.9 47.6 + - - +
343B HIS* 3.0 37.5 + - + -
400B MET* 3.5 5.4 - - + +
401B HIS* 2.7 40.9 + - - +
402B GLY 3.3 8.2 + - - +
403B PRO 3.1 0.6 - - - -
404B ALA* 1.3 74.7 - - + +
406B VAL* 1.3 61.2 + - - +
408B PHE* 3.5 0.5 + - - +
409B THR* 3.1 15.9 + - - -
437B ARG* 4.1 4.1 + - - +
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B MET* 3.8 31.2 - - + -
402B GLY 3.5 13.2 + - - +
403B PRO* 3.1 7.5 + - + +
405B GLU* 1.3 74.7 - - - +
407B ALA* 1.3 53.3 + - - +
409B THR* 3.0 5.7 + - - -
410B CYS* 2.8 34.0 + - - -
429B ILE* 4.8 1.8 - - + -
431B ILE* 4.3 9.9 - - + -
438B THR* 5.2 1.3 - - + +
445B CYS* 3.3 43.3 - - + +
448B ALA* 3.7 8.3 - - + -
449B ALA* 3.7 22.2 - - + -
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B PRO 3.0 12.4 + - - +
404B ALA* 3.4 13.2 - - - +
406B VAL* 1.3 76.5 - - - +
408B PHE* 1.3 52.4 + - - +
410B CYS* 3.3 7.7 + - - +
411B GLU* 2.8 32.6 + - - +
448B ALA* 3.9 14.9 - - + +
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Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.4 50.7 - - + -
49B GLN* 4.0 32.1 - - + +
50B ASN* 3.6 29.4 - - + -
53B LEU* 3.6 28.0 - - + -
343B HIS* 3.2 34.1 - + - -
362B ILE* 4.4 11.0 - - + -
404B ALA 3.1 10.2 + - - +
405B GLU 3.9 2.0 - - - +
406B VAL 3.1 0.4 - - - -
407B ALA* 1.3 71.5 - - - +
409B THR* 1.3 67.2 + - - +
410B CYS 3.2 0.2 + - - -
411B GLU* 3.3 9.8 + - + +
412B LEU* 2.8 30.2 + - + +
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Residues in contact with THR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B HIS* 3.1 28.2 + - - -
397B LYS* 3.7 22.6 - - + -
400B MET* 3.3 13.3 - - - -
405B GLU 3.1 7.0 + - - -
406B VAL 3.0 9.5 + - - -
408B PHE* 1.3 75.1 - - - +
410B CYS* 1.3 62.6 + - - +
412B LEU* 3.2 6.6 + - + +
413B PHE* 3.2 41.6 + - + -
429B ILE* 3.6 24.7 - - + -
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Residues in contact with CYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B VAL* 2.8 18.0 + - - +
407B ALA* 3.5 9.0 - - - +
408B PHE 3.1 0.2 - - - -
409B THR* 1.3 78.3 - - - +
411B GLU* 1.3 61.9 + - - +
413B PHE* 3.4 4.8 - - - +
414B SER* 3.1 21.4 + - - -
429B ILE* 4.9 6.7 - - - -
448B ALA 3.7 14.8 - - - +
449B ALA* 3.6 32.1 - - - -
451B ASP* 5.3 1.3 - - - +
452B ARG* 3.8 31.5 + - - +
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Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 4.4 21.0 - - + +
49B GLN* 5.2 8.3 - - - +
407B ALA 2.8 19.7 + - - +
408B PHE* 3.5 11.2 - - + +
410B CYS* 1.3 73.5 - - - +
412B LEU* 1.3 61.8 + - - +
414B SER* 3.2 11.4 + - - -
415B ARG* 3.0 50.1 + - + +
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.2 3.1 - - + -
46B LEU* 3.9 23.0 - - + +
343B HIS* 5.6 0.9 - - + +
361B GLY 4.0 5.8 - - - +
362B ILE* 3.7 56.1 - - + +
365B ALA* 3.9 17.5 - - + -
397B LYS* 4.7 10.5 - - - +
408B PHE* 2.8 28.1 + - + +
409B THR* 3.2 11.6 + - - +
411B GLU* 1.3 71.4 - - - +
413B PHE* 1.3 58.8 + - + +
415B ARG* 3.1 5.0 + - - +
416B VAL* 2.8 49.7 + - + +
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Residues in contact with PHE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASN* 4.8 1.1 - - - -
365B ALA* 4.1 21.3 - - + -
395B ILE* 3.4 43.1 - - + -
397B LYS* 5.0 4.5 - - + -
409B THR* 3.2 30.5 + - + -
410B CYS* 3.4 10.5 - - - +
412B LEU* 1.3 78.2 - - + +
414B SER* 1.3 59.4 + - - +
416B VAL* 3.4 5.8 + - - +
417B GLU* 2.9 35.0 + - - +
427B MET* 3.5 40.5 - - + +
428B LYS 4.0 6.5 - - - -
429B ILE* 4.2 14.1 - - + -
452B ARG* 3.6 17.9 - - - +
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Residues in contact with SER 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B CYS 3.1 7.8 + - - -
411B GLU* 3.2 20.7 + - - -
413B PHE* 1.3 78.4 - - - +
415B ARG* 1.3 65.4 + - - +
417B GLU* 3.3 13.2 + - - -
418B ASP* 3.2 13.7 + - - -
424B GLN* 2.7 41.8 + - - -
452B ARG* 3.5 8.5 - - - +
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Residues in contact with ARG 415 (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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41B LYS* 3.4 27.1 - - - +
42B VAL* 3.6 24.3 - - + +
45B ASP* 2.7 41.5 + - - +
46B LEU* 3.9 23.3 - - + +
411B GLU* 3.0 38.1 + - + +
412B LEU 3.3 9.0 - - - +
414B SER* 1.3 78.6 - - - +
416B VAL* 1.3 64.1 + - - +
418B ASP* 3.3 23.7 + - - +
419B VAL* 3.3 19.5 + - - +
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Residues in contact with VAL 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.7 2.9 - - + -
365B ALA* 3.7 28.3 - - + +
366B LEU* 3.8 39.5 - - + +
412B LEU* 2.8 28.7 + - + +
413B PHE* 3.8 4.7 - - - +
415B ARG* 1.3 73.6 - - - +
417B GLU* 1.3 59.5 + - - +
419B VAL* 3.3 9.9 + - - +
420B LEU* 2.9 39.7 + - + +
427B MET* 3.7 21.1 - - + -
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B PHE 2.9 18.9 + - - +
414B SER* 3.4 6.3 - - - +
416B VAL* 1.3 76.2 - - - +
418B ASP* 1.3 61.4 + - - +
420B LEU* 3.2 2.0 + - - -
421B GLY 2.7 24.4 + - - -
422B LEU* 2.8 32.5 + - + +
423B PRO 3.7 8.7 - - - +
424B GLN* 3.4 14.6 - - - +
425B ASN 2.9 26.2 + - - -
426B THR* 2.9 0.7 + - - -
427B MET* 2.9 38.7 + - + +
452B ARG* 2.9 29.2 + - - -
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Residues in contact with ASP 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B SER* 3.2 11.4 + - - +
415B ARG* 3.3 21.4 + - - +
417B GLU* 1.3 77.7 - - - +
419B VAL* 1.3 59.3 + - + +
421B GLY* 2.9 21.0 + - - -
422B LEU 5.3 1.8 - - - +
424B GLN* 3.2 18.5 + - - +
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Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.7 18.0 - - - +
34B SER* 4.3 3.0 - - - +
35B PHE* 3.7 31.6 - - + +
38B GLY* 3.6 29.8 - - - -
39B VAL 4.2 0.7 - - - +
42B VAL* 3.7 23.1 - - + -
366B LEU* 4.5 8.7 - - + -
415B ARG 3.3 16.2 - - - +
416B VAL* 3.8 9.9 - - - +
417B GLU 3.3 0.6 - - - -
418B ASP* 1.3 75.7 - - + +
420B LEU* 1.3 63.9 + - + +
421B GLY 3.5 0.2 + - - -
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Residues in contact with LEU 420 (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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30B ILE* 3.2 26.6 - - + +
35B PHE* 4.1 20.0 - - + -
366B LEU* 4.3 3.4 - - + +
369B GLY* 3.3 36.6 - - - +
370B LEU* 3.5 33.9 - - + +
373B ILE* 4.2 8.4 - - + +
416B VAL* 2.9 31.0 + - + +
417B GLU 3.9 0.2 - - - +
419B VAL* 1.3 77.3 - - + +
421B GLY* 1.3 62.5 + - - +
422B LEU* 3.6 36.2 - - + +
427B MET* 4.9 1.3 - - - -
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Residues in contact with GLY 421 (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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417B GLU 2.7 4.6 + - - -
418B ASP* 2.9 15.0 + - - -
419B VAL 3.2 0.6 + - - -
420B LEU* 1.3 80.7 - - - +
422B LEU* 1.3 62.6 + - - +
423B PRO* 4.4 2.8 - - - +
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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