Contacts of the helix formed by residues 385 - 399 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81J ARG* 4.7 12.5 - - - +
83J LYS* 4.4 20.6 - - - +
240J GLU* 5.7 0.2 - - - +
302J ALA* 5.8 5.3 - - - +
303J THR* 5.6 1.7 + - - -
383K ASP 4.3 6.3 + - - +
384K ALA* 1.3 72.8 - - - +
386K PRO* 1.3 68.5 - - - +
387K GLU* 3.1 25.4 - - + +
388K TYR* 3.2 6.1 + - + +
389K ILE* 3.0 22.6 + - - +
428K MET 5.2 1.2 + - - -
429K GLN* 2.7 34.7 + - - +
430K VAL 4.7 1.6 + - - +
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Residues in contact with PRO 386 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J LYS* 5.2 2.7 - - - +
150J VAL* 5.0 5.8 - - + -
152J VAL* 3.9 11.2 - - + -
238J SER* 3.2 28.1 - - - +
239J ALA 3.9 11.4 - - - +
240J GLU* 3.8 31.0 - - + +
371K LYS* 4.9 0.7 - - - -
384K ALA 3.7 4.4 - - - +
385K ASN* 1.3 79.3 - - - +
387K GLU* 1.3 82.0 + - - +
389K ILE* 3.0 13.1 + - + +
390K ALA* 2.7 35.7 + - - +
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Residues in contact with GLU 387 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J ARG* 3.3 44.1 + - - +
83J LYS* 5.0 6.8 - - - -
150J VAL* 5.9 1.7 - - - +
152J VAL* 4.0 18.6 - - + +
158J ILE* 4.3 14.8 - - + +
385K ASN* 3.1 17.3 - - + +
386K PRO* 1.3 109.1 - - - +
388K TYR* 1.3 63.7 + - - +
390K ALA* 3.6 3.5 + - - +
391K GLU* 3.3 23.7 + - - +
429K GLN* 4.4 5.4 - - - +
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Residues in contact with TYR 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337K GLU* 3.5 30.8 - - + +
338K MET 2.9 17.7 + - - -
339K LEU* 3.7 2.1 - - - +
384K ALA* 5.2 0.7 - - + -
385K ASN* 3.2 11.4 + - + +
386K PRO 3.1 0.6 - - - -
387K GLU* 1.3 78.6 - - - +
389K ILE* 1.3 68.6 + - - +
391K GLU* 3.2 12.3 + - + +
392K LEU* 3.1 38.9 + - + +
429K GLN* 3.0 61.4 + - + +
430K VAL 4.0 9.0 - - - -
431K ILE* 3.6 26.5 - - + -
462K PHE* 3.2 22.7 - + - -
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Residues in contact with ILE 389 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J GLN* 4.9 1.6 - - - +
237J VAL* 3.7 39.5 - - + +
238J SER* 3.8 8.5 - - - -
369K PHE* 5.7 4.0 - - + -
371K LYS* 3.8 29.8 - - + -
384K ALA* 3.9 12.3 - - + +
385K ASN 3.0 21.6 + - - +
386K PRO* 3.0 10.0 + - + +
388K TYR* 1.3 72.5 - - - +
390K ALA* 1.3 68.1 + - - +
392K LEU* 2.9 14.0 + - + +
393K ARG* 2.9 24.0 + - + +
431K ILE* 3.5 24.9 - - + -
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Residues in contact with ALA 390 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J VAL* 3.4 33.2 - - + -
153J LYS 3.5 14.4 - - - +
154J LYS* 4.1 6.3 - - - +
156J GLY* 5.2 1.8 - - - -
238J SER* 3.5 15.2 - - - +
386K PRO 2.7 14.0 + - - +
387K GLU 3.7 3.6 - - - +
389K ILE* 1.3 72.5 - - - +
391K GLU* 1.3 64.7 + - + +
393K ARG* 2.9 20.7 + - - +
394K ARG* 2.9 13.9 + - - +
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Residues in contact with GLU 391 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J LYS 4.3 5.9 - - - +
155J ASP 5.2 4.2 - - - +
156J GLY* 5.5 2.9 + - - -
337K GLU* 5.6 4.7 - - - +
387K GLU 3.3 12.7 + - - +
388K TYR* 3.2 18.7 + - + +
389K ILE 3.1 0.4 - - - -
390K ALA* 1.3 78.4 - - - +
392K LEU* 1.3 64.2 + - + +
394K ARG* 3.1 50.4 + - - +
395K ILE* 2.9 34.0 + - + +
465K ASN* 5.4 1.4 - - - +
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Residues in contact with LEU 392 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339K LEU* 4.0 8.1 - - + -
369K PHE* 3.5 27.1 - - + -
388K TYR* 3.1 29.4 + - + +
389K ILE* 2.9 8.8 + - + +
391K GLU* 1.3 76.4 - - - +
393K ARG* 1.3 58.0 + - + +
395K ILE* 3.4 10.2 + - + +
396K LEU* 2.8 38.9 + - + +
431K ILE* 3.5 37.7 - - + -
462K PHE* 3.6 35.7 - - + -
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Residues in contact with ARG 393 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J VAL 3.7 3.2 + - - -
154J LYS* 3.9 29.9 - - + +
232J SER* 5.0 0.4 + - - -
234J GLU* 2.6 45.1 + - - +
235J ASP* 2.8 40.0 + - - +
237J VAL* 4.6 9.2 - - + -
238J SER* 2.7 38.1 + - - +
389K ILE* 2.9 19.9 + - + +
390K ALA* 2.9 18.4 + - - +
392K LEU* 1.3 80.7 - - + +
394K ARG* 1.3 60.1 - - - +
396K LEU* 3.1 5.7 + - - +
397K SER* 2.7 30.8 + - - -
403K TRP* 4.3 18.7 + - + +
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Residues in contact with ARG 394 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J LYS* 3.7 41.0 - - + +
155J ASP* 5.3 7.5 + - - +
390K ALA 2.9 2.9 + - - +
391K GLU* 3.1 42.5 + - - +
393K ARG* 1.3 80.0 - - - +
395K ILE* 1.3 75.2 + - - +
397K SER* 3.0 16.8 + - - -
398K LYS* 3.2 9.8 + - + +
465K ASN* 3.0 35.9 + - - +
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Residues in contact with ILE 395 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391K GLU* 2.9 24.8 + - + +
392K LEU* 3.6 20.6 - - + +
394K ARG* 1.3 82.9 - - - +
396K LEU* 1.3 55.6 + - + +
397K SER 2.7 14.9 + - - -
398K LYS* 3.2 15.1 + - + +
399K GLU* 3.4 17.3 + - + +
461K ALA* 2.9 30.5 - - + +
462K PHE* 4.8 5.4 - - + -
464K ASN 4.3 0.7 - - - +
465K ASN* 2.8 55.2 - - + +
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Residues in contact with LEU 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K LYS* 4.9 1.9 - - - +
367K ILE* 4.6 7.0 - - + -
369K PHE* 3.4 40.4 - - + -
392K LEU* 2.8 26.0 + - + +
393K ARG* 3.4 5.2 - - - +
395K ILE* 1.3 73.6 - - + +
397K SER* 1.3 55.1 + - - +
399K GLU 5.2 0.2 - - - +
400K SER 2.3 27.0 - - - +
401K VAL* 3.3 24.4 - - + +
403K TRP* 4.2 20.8 + - + -
458K GLY* 3.4 40.2 - - - +
461K ALA* 4.4 7.9 - - + +
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Residues in contact with SER 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J LYS* 3.3 24.2 + - - -
5K LEU* 2.5 30.2 - - - +
6K LEU* 4.0 16.0 + - - -
7K LYS* 4.8 4.3 - - - +
393K ARG 2.7 16.1 + - - -
394K ARG* 3.0 12.6 - - - -
395K ILE 2.8 0.4 - - - -
396K LEU* 1.3 82.8 + - - +
398K LYS* 1.3 68.7 + - - +
400K SER* 2.9 13.8 + - - +
403K TRP* 4.9 1.0 + - - -
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Residues in contact with LYS 398 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K LEU* 4.4 13.1 + - - +
394K ARG* 3.2 8.3 + - + +
395K ILE* 3.8 9.4 - - + +
397K SER* 1.3 77.2 - - - +
399K GLU* 1.3 98.6 + - + +
400K SER* 2.8 11.4 + - - -
465K ASN* 6.4 2.9 - - - -
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Residues in contact with GLU 399 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395K ILE* 3.4 10.6 + - + +
398K LYS* 1.3 107.4 + - + +
400K SER* 1.3 70.3 + - - +
401K VAL* 3.5 7.9 + - + +
461K ALA* 3.6 37.5 - - + +
463K LEU* 4.9 10.4 - - + +
464K ASN 6.2 0.4 - - - +
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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