Contacts of the helix formed by residues 342 - 360 (chain A) in PDB entry 2GPV
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 LEU 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ALA* 5.7 0.2 - - + -
265A LEU* 4.2 8.7 - - + -
268A LEU* 3.8 28.9 - - + -
332A MET* 4.4 13.0 - - + -
337A SER* 3.2 8.2 + - - +
340A ALA* 3.2 18.1 - - + +
341A GLY* 1.3 77.0 - - - +
343A LEU* 1.3 58.6 + - - +
344A ASP 3.4 2.0 - - - -
345A LEU* 3.8 15.3 - - + +
346A ASN* 2.8 47.3 + - - +
434A HIS* 3.4 35.0 - - + +
500A OHT 3.7 23.3 - - + -
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLU* 4.4 24.5 - - + +
337A SER* 3.9 17.5 + - - +
338A LYS* 3.9 31.6 - - + +
341A GLY* 3.4 5.2 - - - -
342A LEU* 1.3 74.2 - - - +
344A ASP* 1.3 72.8 + - - +
346A ASN* 4.5 0.6 - - - +
347A ASN* 3.1 51.4 + - - +
343B LEU* 3.9 30.3 - - + -
344B ASP* 5.2 9.6 - - - +
347B ASN* 5.3 2.7 - - - +
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Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLY 5.3 0.6 + - - -
343A LEU* 1.3 80.7 - - - +
345A LEU* 1.3 66.6 + - - +
347A ASN* 3.2 9.5 + - - +
348A ALA* 3.1 22.6 + - - +
434A HIS* 6.5 0.9 - - + -
344B ASP* 4.8 9.5 - - - +
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 3.5 24.3 + - + +
343A LEU 3.4 0.6 - - - -
344A ASP* 1.3 81.2 - - - +
346A ASN* 1.3 63.6 + - - +
348A ALA* 3.2 7.4 + - + +
349A ILE* 3.1 24.3 + - + +
427A THR* 4.7 5.2 - - + +
430A LYS* 4.0 16.6 - - + +
431A ALA* 3.5 31.0 - - + +
434A HIS* 4.1 16.1 - - + +
500A OHT 3.4 58.1 - - + -
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Residues in contact with ASN 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A LEU* 3.1 23.2 - - + +
326A TYR* 2.7 22.4 + - - -
332A MET* 3.8 28.1 + - - +
337A SER* 3.5 26.0 + - - +
342A LEU* 2.8 26.8 + - - +
343A LEU 4.5 1.1 - - - +
345A LEU* 1.3 74.5 - - - +
347A ASN* 1.3 51.1 + - - +
349A ILE* 3.0 9.3 + - - +
350A LEU* 2.7 42.0 + - + +
500A OHT 4.2 5.4 - - - +
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Residues in contact with ASN 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLU* 5.6 2.3 - - - +
343A LEU* 3.1 44.3 + - - +
344A ASP* 3.5 8.1 + - - +
346A ASN* 1.3 75.8 - - - +
348A ALA* 1.3 56.4 + - - +
350A LEU* 3.3 19.8 + - - +
351A GLN* 3.1 24.6 + - - +
338B LYS* 5.1 14.5 - - - +
343B LEU* 5.5 3.6 - - - +
380D MET* 6.2 4.7 - - - -
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A ASP 3.1 8.1 + - - +
345A LEU* 3.3 13.5 - - + +
347A ASN* 1.3 79.2 - - - +
349A ILE* 1.3 61.1 + - - +
351A GLN* 3.1 29.3 + - - +
352A LEU* 3.4 5.5 + - - +
423A LEU* 5.2 2.0 - - + +
427A THR* 4.1 27.3 + - + +
430A LYS* 5.5 11.4 - - + -
380D MET* 6.3 2.5 - - - -
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Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ILE* 4.6 16.4 - - + +
313A VAL* 4.4 11.4 - - + -
314A VAL* 3.7 20.4 - - + -
324A LEU* 3.7 21.3 - - + -
326A TYR* 3.3 25.8 - - + +
345A LEU* 3.1 13.1 + - + +
346A ASN* 3.0 18.2 + - - +
348A ALA* 1.3 72.6 - - - +
350A LEU* 1.3 64.8 + - - +
352A LEU* 3.3 11.7 + - - +
353A VAL* 3.1 19.2 + - - +
427A THR* 4.1 16.6 - - + -
500A OHT 3.8 16.6 - - + -
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASP* 4.0 39.0 - - + +
323A GLU 4.1 8.7 - - - +
324A LEU* 3.9 25.1 - - + -
346A ASN* 2.7 21.6 + - + +
347A ASN* 3.6 22.7 - - - +
348A ALA 3.2 0.2 - - - -
349A ILE* 1.3 75.3 - - - +
351A GLN* 1.3 59.6 + - - +
353A VAL* 3.5 14.8 - - + +
354A LYS* 2.8 29.8 + - - +
357A LYS* 6.3 0.4 - - - +
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Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A ASN 3.1 12.0 + - - +
348A ALA* 3.2 19.9 - - - +
350A LEU* 1.3 76.9 - - - +
352A LEU* 1.3 59.1 + - - +
354A LYS* 3.3 11.0 + - + +
355A LYS* 3.3 22.7 + - - +
423A LEU* 4.0 27.6 - - + +
426A GLN* 5.8 1.0 + - - -
378D ASP* 3.2 29.7 + - - +
379D SER 3.6 14.8 + - - -
380D MET* 3.7 23.5 - - + +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 4.0 23.3 - - + -
314A VAL* 3.8 15.5 - - + -
348A ALA 3.4 4.6 + - - +
349A ILE* 3.3 8.0 + - - +
351A GLN* 1.3 76.9 - - - +
353A VAL* 1.3 63.2 + - - +
355A LYS* 3.6 5.1 + - + +
356A TYR* 3.3 48.0 + - + -
420A THR* 4.4 6.3 - - - +
423A LEU* 4.0 20.9 - - + -
424A LEU* 3.9 33.7 - - + +
427A THR* 3.7 30.3 - - + +
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Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A VAL* 3.6 35.9 - - + +
317A SER* 3.7 26.9 - - - +
318A LEU* 4.2 3.4 - - - +
320A PHE 5.2 0.4 - - - +
323A GLU 5.8 0.2 - - - +
324A LEU* 4.3 9.4 - - + -
349A ILE 3.1 14.8 + - - +
350A LEU* 3.2 18.1 + - + +
352A LEU* 1.3 77.5 - - - +
354A LYS* 1.3 66.6 + - - +
356A TYR* 4.1 0.6 - - - -
357A LYS* 2.9 51.8 + - + +
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Residues in contact with LYS 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A LEU 2.8 17.1 + - - +
351A GLN* 3.7 11.4 - - + +
352A LEU 3.3 0.2 - - - -
353A VAL* 1.3 77.9 - - - +
355A LYS* 1.3 60.7 + - - +
357A LYS* 3.3 14.0 - - + +
358A SER* 2.8 27.3 + - - +
385D VAL* 5.2 20.8 - - - +
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Residues in contact with LYS 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A GLN 3.3 12.6 + - - +
352A LEU* 4.1 6.2 - - + +
353A VAL 3.2 0.6 - - - -
354A LYS* 1.3 79.5 - - - +
356A TYR* 1.3 59.6 + - + +
358A SER* 2.8 34.1 + - - +
359A MET* 3.2 15.2 + - + +
419A MET 3.9 18.4 + - - -
420A THR* 4.0 27.6 - - + +
423A LEU* 4.4 12.9 - - - +
376D ASN* 4.3 6.7 + - - -
378D ASP* 2.7 31.6 + - - -
389D GLN* 4.9 13.5 - - - +
392D GLN* 6.0 4.7 - - - +
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Residues in contact with TYR 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LEU* 3.8 29.1 - - + +
314A VAL* 3.8 15.3 - - + -
318A LEU* 3.7 11.4 - - + +
352A LEU* 3.3 37.6 + - + +
353A VAL 4.3 0.2 - - - +
355A LYS* 1.3 75.1 - - + +
357A LYS* 1.3 66.6 + - - +
359A MET* 3.2 15.8 + - - +
360A LYS 2.9 18.7 + - - -
361A LEU* 3.1 43.2 + - + -
369A LEU* 4.2 23.8 - - + +
417A MET* 4.3 3.4 - - - -
420A THR* 2.4 46.6 + - + -
421A LEU* 5.3 1.0 - - - +
424A LEU* 5.1 5.5 - - - +
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Residues in contact with LYS 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A LEU* 3.3 36.0 - - + +
320A PHE 2.8 30.1 + - - -
321A GLU* 3.7 29.4 + - - +
322A ASP* 4.6 5.5 + - - +
350A LEU* 6.3 0.2 - - - +
353A VAL* 2.9 40.7 + - + +
354A LYS* 3.3 12.4 - - + +
356A TYR* 1.3 75.1 - - - +
358A SER* 1.3 64.5 + - - +
360A LYS* 3.0 19.0 + - - +
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Residues in contact with SER 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A LYS* 2.8 14.8 + - - +
355A LYS* 2.8 22.3 + - - +
357A LYS* 1.3 74.9 - - - +
359A MET* 1.3 64.0 + - - -
360A LYS* 3.4 7.3 + - - +
389D GLN* 5.0 14.2 + - - -
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Residues in contact with MET 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LYS* 3.2 18.8 + - + +
356A TYR* 3.2 19.6 + - + +
358A SER* 1.3 78.1 - - - +
360A LYS* 1.3 65.1 + - - +
361A LEU 4.4 1.8 - - - +
413A ARG* 2.8 40.1 + - + +
416A LYS* 4.2 19.3 - - + +
417A MET* 2.9 58.6 - - + +
420A THR* 4.3 11.7 - - - -
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Residues in contact with LYS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LEU* 5.8 1.1 - - - -
356A TYR 2.9 4.4 + - - -
357A LYS* 3.0 16.1 + - - +
358A SER 4.2 6.1 - - - +
359A MET* 1.3 84.3 - - - +
361A LEU* 1.3 68.6 + - - +
362A GLU* 3.4 12.2 + - - +
413A ARG* 3.3 8.0 + - - +
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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