Contacts of the helix formed by residues 324 - 337 (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 LEU 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A LEU* 3.8 24.2 - - + -
321A SER* 3.3 14.6 - - - +
322A GLY 3.1 1.4 - - - -
323A ASN* 1.3 85.3 - - + +
325A GLN* 1.3 66.5 + - - +
326A GLU 3.2 2.9 - - - -
327A GLU* 3.1 28.4 + - + +
328A CYS* 3.0 21.1 + - - +
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Residues in contact with GLN 325 (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 CYS* 3.3 32.1 + - - +
319A ARG* 5.1 1.1 - - - +
320A GLY 5.1 1.2 + - - -
321A SER* 3.6 11.6 + - - -
322A GLY 3.3 17.4 + - - +
323A ASN 3.5 2.0 - - - -
324A LEU* 1.3 75.5 - - - +
326A GLU* 1.3 66.8 + - + +
328A CYS* 3.1 4.5 + - - +
329A GLU* 2.9 56.9 + - - +
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Residues in contact with GLU 326 (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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323A ASN 5.4 0.4 + - - -
324A LEU 3.2 1.0 - - - -
325A GLN* 1.3 79.4 - - + +
327A GLU* 1.3 66.9 + - - +
329A GLU* 3.3 15.7 + - - +
330A MET* 3.0 24.1 + - - +
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Residues in contact with GLU 327 (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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249A LEU* 4.1 12.0 - - + +
252A ARG* 2.9 30.7 + - - +
324A LEU* 3.1 39.8 + - + +
326A GLU* 1.3 78.0 - - - +
328A CYS* 1.3 63.8 + - - +
330A MET* 3.5 9.2 - - + +
331A LEU* 3.3 20.6 + - - +
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Residues in contact with CYS 328 (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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247A ASN* 4.1 4.7 - - - -
248A CYS* 3.7 21.6 - - - +
249A LEU* 4.0 15.9 - - + +
317A THR 3.9 1.8 - - - -
318A CYS* 2.1 54.1 - - - -
321A SER* 3.1 21.8 - - - +
324A LEU 3.0 9.5 + - - +
325A GLN 3.4 7.4 - - - +
326A GLU 3.1 0.2 - - - -
327A GLU* 1.3 79.3 - - - +
329A GLU* 1.3 62.3 + - - +
331A LEU* 3.2 4.7 + - - +
332A GLU* 3.0 18.5 + - - +
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Residues in contact with GLU 329 (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 CYS* 4.0 10.5 - - + -
325A GLN* 2.9 51.8 + - - +
326A GLU* 3.3 16.5 + - - +
328A CYS* 1.3 77.4 - - - +
330A MET* 1.3 54.1 - - - +
332A GLU* 3.8 3.9 - - - +
333A GLY* 2.7 32.9 + - - -
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Residues in contact with MET 330 (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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326A GLU 3.0 16.5 + - - +
327A GLU* 3.5 11.2 - - + +
329A GLU* 1.3 78.0 - - - +
331A LEU* 1.3 63.2 + - - +
333A GLY* 3.9 0.8 - - - -
334A PHE* 3.2 28.9 + - - +
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Residues in contact with LEU 331 (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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248A CYS* 3.6 33.0 - - + +
249A LEU* 4.0 8.3 - - + -
252A ARG* 3.7 44.6 - - + +
265A LEU* 5.0 2.0 - - + -
269A GLN* 5.0 11.2 - - - +
300A MET* 4.0 22.0 - - + -
314A LEU* 4.7 5.4 - - + -
327A GLU 3.3 9.0 + - - +
328A CYS 3.2 8.7 + - - +
330A MET* 1.3 77.7 - - + +
332A GLU* 1.3 69.0 + - - +
334A PHE* 3.2 20.4 + - + +
335A PHE* 3.6 18.1 - - + -
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Residues in contact with GLU 332 (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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248A CYS* 3.9 21.3 - - - -
313A ALA* 4.0 14.4 - - - +
314A LEU* 5.0 8.7 + - + +
316A CYS* 4.5 8.7 - - - +
317A THR* 5.9 0.4 - - - -
318A CYS* 4.0 13.7 - - - +
328A CYS 3.0 16.2 + - - +
329A GLU* 3.8 4.8 - - - +
331A LEU* 1.3 77.6 - - - +
333A GLY* 1.3 61.0 + - - +
335A PHE* 3.1 11.4 + - - +
336A SER* 2.5 60.6 + - - -
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Residues in contact with GLY 333 (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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329A GLU 2.7 22.8 + - - -
330A MET* 3.9 1.1 - - - -
332A GLU* 1.3 70.6 + - - +
334A PHE* 1.3 58.7 + - - +
335A PHE 3.0 6.1 - - - -
336A SER* 3.5 11.4 - - - -
337A HIS* 2.9 40.0 + - - +
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Residues in contact with PHE 334 (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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268A PHE* 3.1 53.8 - + - -
269A GLN* 3.7 27.1 - - + -
272A CYS 3.7 4.3 - - - -
273A HIS* 3.6 45.5 - + - -
274A PRO* 4.3 4.7 - - + -
330A MET* 3.2 20.4 + - - +
331A LEU* 3.4 15.7 - - + +
332A GLU 3.2 0.6 - - - -
333A GLY* 1.3 75.6 - - - +
335A PHE* 1.3 60.0 + + + +
338A ASN* 2.9 39.6 - - - +
341A LEU* 4.5 0.5 - - - +
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Residues in contact with PHE 335 (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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265A LEU* 4.1 13.9 - - + -
268A PHE* 3.4 37.7 - + - -
292A TYR* 4.4 5.6 - + - -
295A LEU* 3.7 21.8 - - + -
300A MET* 4.7 1.8 - - + -
302A PRO* 3.9 24.9 - - + -
312A VAL* 3.5 22.0 - - + +
313A ALA* 4.4 3.1 - - - +
314A LEU* 3.6 54.1 - - + +
331A LEU* 3.6 22.2 - - + -
332A GLU 3.1 6.1 + - - +
334A PHE* 1.3 83.1 - + + +
336A SER* 1.3 63.6 + - - +
337A HIS 3.5 1.4 + - - -
338A ASN* 4.7 2.1 + - - +
341A LEU* 3.9 10.3 - - + +
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Residues in contact with SER 336 (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 SER* 5.3 7.4 - - - -
312A VAL 3.3 18.4 + - - +
313A ALA* 4.4 4.7 - - - -
332A GLU* 2.5 47.7 + - - -
333A GLY* 3.5 4.3 - - - -
335A PHE* 1.3 78.6 - - - +
337A HIS* 1.3 65.1 + - - +
338A ASN 4.0 0.4 - - - -
342A THR* 5.5 1.5 + - - -
1E NAG 6.2 0.5 - - - +
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Residues in contact with HIS 337 (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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333A GLY* 2.9 19.0 + - - +
336A SER* 1.3 82.6 + - - +
338A ASN* 1.3 57.9 + - - +
339A PRO* 4.2 9.4 - - + +
342A THR* 5.4 2.0 - - - -
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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