Contacts of the helix formed by residues 338 - 356 (chain A) in PDB entry 2GH0
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 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A CYS* 3.0 19.8 + - - +
274A PRO* 3.7 13.3 - - - +
333A GLY 4.0 0.2 - - - +
334A PHE* 2.9 45.4 - - - +
335A PHE 4.7 3.3 + - - +
336A SER 4.0 0.4 - - - -
337A HIS* 1.3 75.3 - - - +
339A PRO* 1.4 61.8 - - - +
340A CYS* 3.0 24.4 - - - +
341A LEU* 3.3 19.9 - - + +
342A THR* 2.9 32.4 + - - -
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Residues in contact with PRO 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A PRO* 3.9 19.1 - - + -
276A ASP 4.6 1.3 - - - +
277A ILE* 4.1 16.4 - - + +
278A LEU 4.3 3.4 - - - +
279A GLY* 3.6 25.3 - - - +
337A HIS* 4.2 11.0 - - + +
338A ASN* 1.4 86.9 - - - +
340A CYS* 1.3 58.7 + - - +
342A THR* 4.2 6.7 - - - -
343A GLU* 2.9 37.0 + - + +
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Residues in contact with CYS 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A CYS* 3.5 30.1 - - - +
274A PRO* 4.0 11.2 - - + -
279A GLY* 3.2 17.7 - - - +
281A CYS* 2.1 56.1 - - - -
288A CYS* 3.8 4.9 - - - -
338A ASN* 3.0 11.2 - - - +
339A PRO* 1.3 80.9 - - - +
341A LEU* 1.3 59.5 + - - +
343A GLU* 3.9 1.4 - - - +
344A ALA* 2.9 31.5 + - - +
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A PHE* 4.2 12.6 - - + -
272A CYS* 4.5 2.7 - - + -
288A CYS* 3.9 25.8 - - - -
289A LEU* 4.6 3.6 - - + -
292A TYR* 3.8 44.2 - - + -
312A VAL* 4.0 7.0 - - + -
334A PHE 4.5 1.1 - - - +
335A PHE* 3.9 24.2 - - - +
338A ASN* 3.2 21.0 + - - +
340A CYS* 1.3 81.2 - - - +
342A THR* 1.3 63.3 + - - +
344A ALA* 3.4 0.9 + - - +
345A ILE* 3.0 43.2 + - + +
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Residues in contact with THR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A THR* 6.0 1.6 - - - +
336A SER 5.5 1.4 + - - -
337A HIS* 5.4 1.6 - - - -
338A ASN 2.9 23.0 + - - -
339A PRO* 3.9 7.9 - - - -
341A LEU* 1.3 78.8 - - - +
343A GLU* 1.3 70.7 + - - +
345A ILE* 3.5 5.8 + - - +
346A ALA* 2.9 29.7 + - + +
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Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU 4.3 16.2 - - - +
279A GLY 4.7 6.3 - - - +
285A GLN* 3.8 13.4 + - - +
339A PRO* 2.9 21.9 + - + +
340A CYS 4.0 2.0 - - - +
342A THR* 1.3 87.9 - - - +
344A ALA* 1.3 61.4 + - - +
346A ALA* 3.7 4.5 - - - +
347A ALA* 3.0 31.7 + - - +
350A ARG* 3.3 25.9 + - - -
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Residues in contact with ALA 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A CYS* 4.7 0.4 - - - -
285A GLN* 3.8 39.0 - - + +
288A CYS* 4.5 5.6 - - - -
289A LEU* 3.6 25.7 - - + +
340A CYS 2.9 19.9 + - - +
341A LEU* 3.7 4.3 - - - +
343A GLU* 1.3 77.1 - - - +
345A ILE* 1.3 62.1 + - - +
347A ALA* 4.0 2.1 - - - +
348A LYS* 3.2 22.9 + - - +
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Residues in contact with ILE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 4.4 16.6 - - + -
289A LEU* 3.7 20.4 - - + -
292A TYR* 4.4 17.5 - - + -
304A PHE* 4.9 3.4 - - + -
310A THR* 5.2 8.7 - - - +
312A VAL* 4.4 20.4 - - + -
341A LEU* 3.0 40.1 + - + +
342A THR* 4.0 5.4 - - - +
344A ALA* 1.3 77.3 - - - +
346A ALA* 1.3 58.0 + - - +
348A LYS* 3.2 5.6 + - - +
349A MET* 2.9 58.0 + - + +
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A THR* 2.9 21.9 + - + +
343A GLU* 3.7 8.5 - - - +
345A ILE* 1.3 78.1 - - - +
347A ALA* 1.3 58.7 + - - +
349A MET* 3.3 9.2 + - - +
350A ARG* 2.9 53.6 + - - +
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLN* 3.7 21.3 - - - +
343A GLU 3.0 17.8 + - - +
344A ALA 4.0 1.6 - - - +
345A ILE 3.3 0.2 - - - -
346A ALA* 1.3 77.3 - - - +
348A LYS* 1.3 57.4 + - - +
350A ARG* 3.3 28.5 + - - +
351A PHE* 2.9 27.2 + - - +
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Residues in contact with LYS 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLN* 3.7 22.5 + - + +
217A LEU* 4.2 12.1 - - + -
286A SER* 6.3 2.4 - - - +
289A LEU* 3.9 20.9 - - + -
344A ALA 3.2 15.8 + - - +
345A ILE* 3.6 4.9 - - - +
347A ALA* 1.3 79.2 - - - +
349A MET* 1.3 60.0 + - - +
351A PHE* 3.2 26.2 + - + +
352A HIS* 2.9 60.7 + - + +
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Residues in contact with MET 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.2 26.0 - - + +
218A CYS 3.7 9.4 - - - +
219A PRO* 3.6 12.8 - - + +
231A ARG* 3.6 24.0 - - - +
304A PHE* 3.8 24.9 - - + -
310A THR* 3.7 22.2 - - + -
345A ILE* 2.9 41.3 + - + +
346A ALA* 3.7 7.9 - - - +
348A LYS* 1.3 77.9 - - - +
350A ARG* 1.3 61.5 + - - +
352A HIS* 3.2 4.8 + - - +
353A SER* 3.0 25.7 + - - -
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Residues in contact with ARG 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLU* 3.3 26.5 + - - -
346A ALA* 2.9 32.6 + - - +
347A ALA* 3.3 31.5 + - - +
349A MET* 1.3 68.7 - - - +
351A PHE* 1.3 67.3 + - - +
353A SER* 3.2 7.8 + - - -
354A GLN* 3.0 43.8 + - - +
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Residues in contact with PHE 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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210A PRO* 6.4 1.8 - - + -
347A ALA 2.9 13.5 + - - +
348A LYS* 3.2 29.1 + - + +
350A ARG* 1.3 75.3 - - - +
352A HIS* 1.3 81.8 + + - +
354A GLN* 3.1 16.2 + - + +
355A LEU* 2.9 61.4 + - + +
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Residues in contact with HIS 352 (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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161A LEU* 4.2 0.2 - - - +
165A PHE* 3.6 42.9 - + + -
210A PRO* 4.7 3.6 + - - +
213A GLN* 3.2 29.8 - - - +
214A GLY* 3.4 15.3 + - - -
217A LEU 2.8 20.7 + - - -
218A CYS* 4.3 0.8 - - - -
219A PRO* 3.6 13.0 - - + -
348A LYS* 2.9 35.1 + - + +
349A MET 3.5 7.9 - - - +
351A PHE* 1.3 96.8 - + - +
353A SER* 1.3 61.5 + - - +
354A GLN 3.3 0.5 + - - -
355A LEU* 3.5 2.5 + - + +
356A PHE* 3.5 16.5 + - - +
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Residues in contact with SER 353 (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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161A LEU* 3.8 15.1 - - - +
219A PRO* 3.2 23.5 - - - +
349A MET 3.0 10.8 + - - -
350A ARG* 3.2 10.8 + - - -
352A HIS* 1.3 74.6 - - - +
354A GLN* 1.3 60.8 + - - +
356A PHE* 3.5 4.2 + - - +
357A SER* 3.2 26.0 + - - -
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Residues in contact with GLN 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 ARG* 3.0 40.7 + - - +
351A PHE* 3.5 14.6 - - + +
353A SER* 1.3 76.7 - - - +
355A LEU* 1.3 65.6 + - - +
356A PHE 3.1 2.5 - - - -
357A SER* 3.0 26.6 + - - +
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Residues in contact with LEU 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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165A PHE* 4.3 21.5 - - + -
168A LEU* 5.1 7.9 - - + -
351A PHE* 2.9 48.6 + - + +
352A HIS* 3.8 7.0 - - + +
354A GLN* 1.3 77.6 - - - +
356A PHE* 1.3 64.5 + - + +
357A SER 3.7 3.1 + - - +
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Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.9 21.3 - - + -
164A LYS* 3.7 48.3 + - + +
165A PHE* 3.4 52.0 - + - -
168A LEU* 4.3 22.2 - - + -
352A HIS 3.5 7.1 + - - +
353A SER 3.7 3.8 - - - +
354A GLN 3.1 0.2 - - - -
355A LEU* 1.3 84.7 - - + +
357A SER* 1.3 62.7 + - - +
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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