Contacts of the helix formed by residues 342 - 353 (chain A) in PDB entry 2G4C
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
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Residue Dist Surf HB Arom Phob DC
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107A ARG* 4.4 11.4 - - + -
110A LEU* 3.9 25.8 - - + +
111A ALA* 3.9 34.1 - - + +
114A TRP* 4.9 9.9 - - + -
211A ILE* 4.1 14.8 - - + -
235A THR* 2.9 40.1 + - + +
237A ALA* 4.3 19.3 - - + -
262A TRP* 5.1 2.9 - - + -
263A TRP* 5.2 7.2 - - + -
340A GLY* 3.5 2.4 + - - +
341A ASP* 1.3 71.7 - - - +
343A ASP* 1.3 56.3 + - - +
345A GLY* 3.4 2.0 - - - +
346A MET* 2.6 37.3 + - - +
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Residues in contact with ASP 343 (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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91A LEU 6.1 0.2 - - - +
96A HIS* 4.8 9.9 + - + -
99A PHE* 3.0 27.5 - - + -
107A ARG* 2.7 34.9 + - - -
233A GLU 4.4 2.8 - - - +
234A LYS* 3.6 11.5 - - + +
235A THR* 2.7 33.7 + - - +
341A ASP* 3.4 5.5 + - - +
342A LEU* 1.3 76.5 - - - +
344A ARG* 1.3 58.0 + - - +
346A MET* 3.0 20.9 - - - +
347A LEU* 3.2 15.7 - - - +
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Residues in contact with ARG 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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92A LEU* 2.6 62.6 + - + +
234A LYS* 3.1 16.1 - - - +
293A PHE* 4.1 7.1 - - + -
298A GLU* 3.9 19.0 + - - +
299A LEU* 3.0 36.0 + - - +
300A ILE* 4.0 11.2 - - + +
341A ASP* 3.0 28.1 + - + +
342A LEU 3.2 0.2 - - - -
343A ASP* 1.3 74.9 - - - +
345A GLY* 1.3 61.4 + - - +
346A MET 3.1 1.6 - - - -
347A LEU* 3.4 9.5 + - + +
348A ALA* 2.9 27.5 + - - +
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Residues in contact with GLY 345 (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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110A LEU* 4.1 7.0 - - - -
263A TRP* 3.4 28.5 - - - -
300A ILE* 4.7 2.2 - - - +
341A ASP 2.9 14.4 + - - -
342A LEU* 3.1 4.7 + - - -
344A ARG* 1.3 74.0 - - - +
346A MET* 1.3 68.7 + - - +
348A ALA* 3.5 5.4 - - - +
349A TYR* 3.2 26.4 + - - -
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Residues in contact with MET 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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78A PHE 5.2 0.7 - - - +
79A LEU* 5.5 0.9 - - + -
99A PHE* 3.4 31.6 - - + -
103A GLY* 3.3 34.5 - - - +
106A LEU* 3.3 38.0 - - + +
107A ARG* 3.6 21.5 - - + -
110A LEU* 4.0 7.8 - - + +
342A LEU 2.6 15.0 + - - +
343A ASP* 3.0 18.6 - - - +
345A GLY* 1.3 75.2 - - - +
347A LEU* 1.3 56.4 + - + +
349A TYR* 2.7 29.6 + - - +
350A LEU* 3.1 22.1 + - + +
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Residues in contact with LEU 347 (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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70A LEU* 6.2 0.9 - - + -
79A LEU* 4.3 17.9 - - + -
91A LEU* 4.0 54.7 - - + +
92A LEU* 4.2 17.9 - - + -
99A PHE* 5.1 4.7 - - + -
293A PHE* 4.1 11.0 - - + -
343A ASP 3.2 18.8 - - - +
344A ARG* 3.5 15.9 - - + +
346A MET* 1.3 79.1 - - + +
348A ALA* 1.3 58.1 + - - +
350A LEU* 2.6 33.5 + - + +
351A TYR* 2.8 23.9 + - + +
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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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273A PHE* 4.0 13.5 - - + -
291A TYR* 3.3 46.1 - - + -
293A PHE* 4.0 4.2 - - + -
300A ILE* 5.0 2.5 - - + -
344A ARG 2.9 20.6 + - - +
345A GLY* 3.5 11.9 - - - +
347A LEU* 1.3 70.8 - - - +
349A TYR* 1.3 59.4 + - - +
351A TYR 3.5 0.3 + - - -
352A ASP* 3.0 30.4 + - - +
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Residues in contact with TYR 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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106A LEU* 5.2 5.4 - - + -
110A LEU* 4.1 17.5 - - + -
262A TRP* 5.2 0.6 - + - -
263A TRP* 2.3 62.3 + + - -
266A PHE* 3.6 42.0 - + + +
267A ALA* 3.9 5.8 - - + -
273A PHE* 4.2 9.2 - + - -
345A GLY 3.2 17.5 + - - -
346A MET* 2.7 17.9 + - - +
348A ALA* 1.3 75.9 - - + +
350A LEU* 1.3 62.0 + - - +
352A ASP* 3.4 10.9 + - + +
353A SER* 3.2 25.1 + - - -
374A LEU* 3.7 18.0 - - + +
375A HIS 6.3 0.4 - - - -
378A LEU* 3.9 22.4 - - + -
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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
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69A LEU* 3.3 22.2 - - + +
73A CYS* 3.6 28.0 - - - -
78A PHE* 3.9 18.4 - - + -
79A LEU* 3.8 16.8 - - + -
106A LEU* 3.9 15.0 - - + -
346A MET* 3.1 16.7 + - + +
347A LEU* 2.6 18.8 + - + +
349A TYR* 1.3 74.1 - - - +
351A TYR* 1.3 59.6 + - + +
353A SER* 3.2 12.0 + - - +
354A PHE 3.9 1.2 + - - -
372A LEU* 3.8 19.5 - - + -
374A LEU* 3.6 31.6 - - + -
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Residues in contact with TYR 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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67A GLU* 3.1 41.8 + - + -
69A LEU* 3.4 19.7 - - + -
70A LEU* 3.5 23.5 - - + +
91A LEU* 5.7 2.6 - - + +
291A TYR* 4.2 12.8 - - + +
293A PHE* 3.7 27.1 - + - -
294A PRO* 3.7 31.0 - - + -
295A TRP* 3.6 21.0 - + - -
347A LEU* 2.8 22.9 + - + +
348A ALA 3.8 4.0 - - - +
350A LEU* 1.3 75.4 - - + +
352A ASP* 1.3 59.4 + - - +
353A SER 3.0 10.3 + - - -
354A PHE* 3.0 19.9 + - - +
355A GLN 4.6 1.1 + - - -
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Residues in contact with ASP 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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266A PHE 4.5 0.7 - - - +
267A ALA* 3.4 12.7 - - - -
268A MET* 2.8 41.8 + - - +
269A SER* 3.4 34.2 + - - +
272A ASN* 4.8 0.3 + - - -
273A PHE* 4.8 3.8 - - + -
291A TYR* 3.6 19.0 + - + +
348A ALA 3.0 18.4 + - - +
349A TYR* 3.4 13.8 + - + +
351A TYR* 1.3 76.6 - - - +
353A SER* 1.3 56.7 + - - +
354A PHE 3.5 3.7 + - - +
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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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268A MET* 4.9 5.3 - - - +
349A TYR 3.2 12.1 + - - -
350A LEU* 3.2 17.5 + - - -
351A TYR 3.0 0.4 + - - -
352A ASP* 1.3 77.6 - - - +
354A PHE* 1.3 59.2 + - - +
371A VAL* 3.6 4.3 - - - +
372A LEU* 3.6 15.8 - - - +
373A LYS* 3.1 41.1 + - - +
374A LEU* 3.6 23.5 - - - +
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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