Contacts of the helix formed by residues 349 - 359 (chain A) in PDB entry 2GC5
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 ALA 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A TYR* 1.3 69.1 - - + +
350A ALA* 1.3 65.6 + - - +
351A MET 3.3 0.4 - - - -
352A ALA* 3.6 13.4 + - - +
353A ASP* 3.1 24.3 + - - +
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Residues in contact with ALA 350 (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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348A TYR 2.5 13.2 + - - +
349A ALA* 1.3 73.7 - - - +
351A MET* 1.3 59.7 + - + +
353A ASP* 3.4 6.1 + - - +
354A ARG* 2.9 31.1 + - - +
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Residues in contact with MET 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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316A HIS 4.2 18.6 - - - +
318A PRO* 3.9 22.0 - - + +
321A ILE* 3.8 38.9 - - + +
342A ILE* 4.5 22.9 - - + -
348A TYR* 3.2 30.3 - - - +
349A ALA 3.3 0.2 - - - -
350A ALA* 1.3 77.6 - - + +
352A ALA* 1.3 55.7 + - - +
354A ARG* 3.3 8.0 + - - +
355A LEU* 3.0 36.2 + - + +
411A GLY* 5.6 4.9 - - - +
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Residues in contact with ALA 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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348A TYR* 4.9 0.4 - - - -
349A ALA* 3.6 16.6 + - - +
350A ALA 3.4 0.2 - - - -
351A MET* 1.3 76.2 - - - +
353A ASP* 1.3 60.3 + - - +
355A LEU* 3.9 6.5 - - - +
356A THR* 3.0 33.8 + - + +
362A VAL* 4.9 0.7 - - - +
364A LEU* 3.8 40.2 - - + -
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Residues in contact with ASP 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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349A ALA 3.1 18.2 + - - +
350A ALA* 3.7 6.7 - - - +
351A MET 3.3 0.2 - - - -
352A ALA* 1.3 73.9 - - - +
354A ARG* 1.3 61.1 + - - +
355A LEU 3.2 0.2 - - - -
356A THR* 3.3 7.6 + - - -
357A ALA* 3.1 32.9 + - - +
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Residues in contact with ARG 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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321A ILE* 5.3 2.5 - - + -
322A ASN* 4.6 11.2 - - - +
325A ILE* 3.5 20.8 - - + +
350A ALA 2.9 17.3 + - - +
351A MET* 3.4 9.6 - - - +
353A ASP* 1.3 76.0 - - - +
355A LEU* 1.3 59.7 + - - +
357A ALA* 4.2 4.1 - - - +
358A ALA* 3.5 22.7 + - - +
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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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321A ILE* 3.7 31.6 - - + -
324A LEU* 5.0 5.8 - - + -
325A ILE* 3.9 8.3 - - + -
328A LEU* 5.9 0.2 - - + -
338A VAL* 4.4 14.1 - - + -
340A ALA* 3.8 28.9 - - + -
342A ILE* 6.4 0.2 - - + -
351A MET* 3.0 20.4 + - + +
352A ALA* 4.1 4.7 - - - +
353A ASP 3.2 0.2 - - - -
354A ARG* 1.3 74.3 - - - +
356A THR* 1.3 58.6 + - - +
357A ALA 3.2 2.0 - - - -
358A ALA 3.2 0.3 + - - -
359A PHE* 2.9 56.4 + - + +
362A VAL* 3.4 25.3 - - + +
364A LEU* 5.6 0.4 - - + -
410A THR* 5.1 2.7 - - + -
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Residues in contact with THR 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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352A ALA* 3.0 20.8 + - + +
353A ASP* 3.3 12.5 + - - -
355A LEU* 1.3 75.3 - - - +
357A ALA* 1.3 57.4 - - - +
359A PHE 3.1 16.7 - - - +
360A SER 5.3 0.3 - - - +
362A VAL* 3.7 27.8 - - + -
364A LEU* 5.9 2.9 - - + -
386A ARG* 3.8 28.0 + - - +
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Residues in contact with ALA 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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353A ASP 3.1 18.8 + - - +
354A ARG* 4.2 5.8 - - - +
355A LEU 3.2 0.2 - - - -
356A THR* 1.3 77.3 + - - +
358A ALA* 1.3 59.8 + - + +
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Residues in contact with ALA 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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325A ILE* 3.6 29.6 - - + -
329A LYS* 5.5 7.9 - - + +
354A ARG 3.5 17.6 + - - +
355A LEU 3.2 1.2 + - - -
357A ALA* 1.3 81.5 - - - +
359A PHE* 1.3 77.9 + - + +
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Residues in contact with PHE 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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325A ILE* 3.9 29.8 - - + -
328A LEU* 3.6 38.4 - - + -
329A LYS* 4.7 10.3 - - + -
332A PHE* 6.4 0.7 - - + -
336A ILE* 3.7 29.6 - - + +
338A VAL* 3.6 25.1 - - + -
355A LEU* 2.9 37.1 + - + +
356A THR* 3.1 21.3 - - - +
357A ALA 3.6 0.2 - - - -
358A ALA* 1.3 90.4 - - + +
360A SER* 1.3 68.7 + - - +
361A THR 3.5 0.6 + - - -
362A VAL* 4.1 6.8 - - + +
386A ARG* 5.2 0.3 + - - -
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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