Contacts of the helix formed by residues 385 - 399 (chain H) in PDB entry 2GLJ
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 ASN 385 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81G ARG* 4.6 13.6 - - - +
83G LYS* 4.3 20.8 - - - +
302G ALA* 5.7 6.7 - - - +
303G THR* 5.5 2.6 + - - +
383H ASP 4.3 6.6 + - - +
384H ALA* 1.3 73.6 - - - +
386H PRO* 1.3 67.8 - - - +
387H GLU* 3.1 24.9 - - + +
388H TYR* 3.1 7.6 + - + +
389H ILE* 3.0 22.2 + - - +
428H MET 5.2 1.0 + - - -
429H GLN* 2.7 35.0 + - - +
430H VAL 4.7 2.4 + - - +
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Residues in contact with PRO 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G LYS* 5.1 3.4 - - - +
150G VAL* 5.0 6.7 - - + -
152G VAL* 4.0 11.2 - - + -
238G SER* 3.4 27.4 - - - +
239G ALA 3.8 10.1 - - - +
240G GLU* 3.7 32.3 - - + +
371H LYS* 4.8 1.3 - - - -
384H ALA 3.7 3.1 - - - +
385H ASN* 1.3 79.9 - - + +
387H GLU* 1.3 80.7 + - - +
389H ILE* 2.9 13.8 + - + +
390H ALA* 2.7 36.0 + - - +
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Residues in contact with GLU 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G ARG* 3.3 46.8 + - - +
83G LYS* 4.9 6.9 - - - -
150G VAL* 5.9 1.4 - - - +
152G VAL* 4.0 18.9 - - + +
158G ILE* 4.3 13.8 - - + +
385H ASN* 3.1 17.6 - - + +
386H PRO* 1.3 108.4 - - - +
388H TYR* 1.3 63.9 + - - +
390H ALA* 3.6 3.1 + - - +
391H GLU* 3.3 23.6 + - - +
429H GLN* 4.4 4.9 - - - +
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Residues in contact with TYR 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337H GLU* 3.6 29.2 - - + +
338H MET 3.0 16.9 + - - -
339H LEU* 3.6 1.9 - - - +
384H ALA* 5.2 0.9 - - + -
385H ASN* 3.1 12.2 + - + +
386H PRO 3.1 0.6 - - - -
387H GLU* 1.3 78.7 - - - +
389H ILE* 1.3 67.0 + - - +
391H GLU* 3.2 12.9 + - + +
392H LEU* 3.1 37.1 + - + +
429H GLN* 3.1 62.0 + - + +
430H VAL 4.0 8.3 - - - -
431H ILE* 3.5 27.4 - - + -
462H PHE* 3.1 24.6 - + - -
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Residues in contact with ILE 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G GLN* 4.9 1.6 - - - +
237G VAL* 3.7 35.2 - - + +
238G SER* 3.9 6.7 - - - -
369H PHE* 5.7 3.8 - - + -
371H LYS* 3.8 35.7 - - + -
384H ALA* 3.9 11.7 - - + +
385H ASN 3.0 19.8 + - - +
386H PRO* 2.9 12.9 + - + +
388H TYR* 1.3 73.6 - - - +
390H ALA* 1.3 67.7 + - - +
392H LEU* 2.9 14.6 + - + +
393H ARG* 2.9 22.7 + - + +
431H ILE* 3.6 24.7 - - + -
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Residues in contact with ALA 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G VAL* 3.4 33.0 - - + -
153G LYS 3.6 12.6 - - - +
154G LYS* 4.2 7.4 - - - +
156G GLY* 5.3 2.5 - - - -
238G SER* 3.5 15.4 - - - +
386H PRO 2.7 13.8 + - - +
387H GLU 3.8 3.8 - - - +
389H ILE* 1.3 73.1 - - - +
391H GLU* 1.3 65.7 + - + +
393H ARG* 2.9 19.4 + - - +
394H ARG* 2.9 13.7 + - - +
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Residues in contact with GLU 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G LYS 4.4 5.2 - - - +
155G ASP 5.3 4.0 - - - +
156G GLY* 5.6 2.6 + - - -
337H GLU* 5.6 4.7 - - - +
387H GLU 3.3 12.0 + - - +
388H TYR* 3.2 19.4 + - + +
389H ILE 3.1 0.4 - - - -
390H ALA* 1.3 79.4 - - - +
392H LEU* 1.3 63.6 + - + +
394H ARG* 3.1 51.3 + - - +
395H ILE* 2.9 33.7 + - + +
465H ASN* 4.9 2.9 - - - +
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Residues in contact with LEU 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339H LEU* 4.0 8.1 - - + -
369H PHE* 3.6 27.8 - - + -
388H TYR* 3.1 29.6 + - + +
389H ILE* 2.9 8.6 + - + +
391H GLU* 1.3 75.9 - - + +
393H ARG* 1.3 57.7 + - + +
395H ILE* 3.3 10.2 + - + +
396H LEU* 2.8 39.7 + - + +
431H ILE* 3.5 37.9 - - + -
462H PHE* 3.6 36.8 - - + -
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Residues in contact with ARG 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G VAL 3.7 3.2 + - - -
154G LYS* 4.0 28.1 - - + +
232G SER* 5.2 0.2 + - - -
234G GLU* 2.7 45.8 + - - +
235G ASP* 2.8 40.2 + - - +
237G VAL* 4.5 9.6 - - + -
238G SER* 2.6 39.0 + - - +
389H ILE* 2.9 21.4 + - + +
390H ALA* 2.9 17.5 + - - +
392H LEU* 1.3 79.5 - - + +
394H ARG* 1.3 60.2 + - - +
396H LEU* 3.1 10.9 + - - +
397H SER* 2.7 25.4 + - - -
403H TRP* 4.2 20.7 + - + +
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Residues in contact with ARG 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G LYS* 3.7 41.6 - - + +
155G ASP* 5.3 8.4 + - - +
390H ALA 2.9 3.3 + - - +
391H GLU* 3.1 43.9 + - - +
393H ARG* 1.3 79.5 - - - +
395H ILE* 1.3 75.8 + - - +
397H SER* 3.0 17.5 + - - -
398H LYS* 3.1 10.0 + - + +
465H ASN* 3.8 30.6 + - - +
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Residues in contact with ILE 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H LYS* 5.0 2.0 - - - +
391H GLU* 2.9 24.1 + - + +
392H LEU* 3.6 20.6 - - + +
394H ARG* 1.3 86.7 - - - +
396H LEU* 1.3 61.6 + - + +
397H SER 2.8 10.8 + - - -
398H LYS* 3.2 15.1 + - + +
399H GLU* 3.3 16.7 + - + +
461H ALA* 2.8 31.6 - - + +
462H PHE* 4.7 10.5 - - + -
464H ASN 4.8 8.3 - - - +
465H ASN* 4.1 24.5 - - + +
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Residues in contact with LEU 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367H ILE* 4.6 6.7 - - + -
369H PHE* 3.4 39.5 - - + -
392H LEU* 2.8 28.6 + - + +
393H ARG* 3.1 5.8 + - - +
395H ILE* 1.3 73.2 - - + +
397H SER* 1.3 54.2 + - - +
400H SER 2.3 27.9 - - - +
401H VAL* 3.3 23.9 - - + +
403H TRP* 4.2 21.8 + - + -
458H GLY* 3.4 40.6 - - - +
461H ALA* 4.3 8.5 - - + +
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Residues in contact with SER 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G LYS* 3.3 22.9 + - - -
393H ARG 2.7 15.6 + - - -
394H ARG* 3.0 12.3 - - - -
395H ILE 2.8 0.4 - - - -
396H LEU* 1.3 81.0 + - - +
398H LYS* 1.3 69.5 + - - +
400H SER* 2.9 13.9 + - - +
403H TRP* 5.0 5.0 + - - -
209O LYS* 4.0 34.0 + - - +
211O GLY* 5.0 1.9 - - - -
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Residues in contact with LYS 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394H ARG* 3.1 7.8 + - + +
395H ILE* 3.8 8.7 - - + +
397H SER* 1.3 77.4 - - - +
399H GLU* 1.3 99.1 + - + +
400H SER* 2.8 9.9 + - - -
209O LYS 5.0 4.5 - - - -
210O ASP 4.3 14.2 + - - +
211O GLY* 4.4 7.1 - - - -
212O GLU* 4.4 22.0 + - - +
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Residues in contact with GLU 399 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395H ILE* 3.3 9.5 + - + +
398H LYS* 1.3 107.9 + - + +
400H SER* 1.3 70.8 + - - +
401H VAL* 3.5 7.4 + - - +
461H ALA* 3.6 36.8 - - + +
463H LEU* 4.9 10.0 - - + +
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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
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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