Contacts of the helix formed by residues 329 - 338 (chain A) in PDB entry 4Y05
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 329 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A TYR* 3.3 12.8 + - + -
328A THR* 1.3 82.2 + - - +
330A ALA* 1.3 60.9 + - - +
332A LEU* 2.9 23.7 + - - +
333A VAL* 3.4 8.1 + - - +
344A CYS* 4.2 10.3 - - - -
373A ILE* 3.6 31.0 - - + -
377A ALA* 5.2 0.2 - - + -
488A PHE* 3.6 25.5 - - + -
490A LEU* 4.6 0.7 - - + -
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Residues in contact with ALA 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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254A ILE* 5.3 5.6 - - + -
325A TYR* 3.0 49.9 + - + +
326A ARG* 3.7 11.9 - - - +
329A ALA* 1.3 74.9 - - - +
331A PRO* 1.4 65.1 - - + +
332A LEU 3.0 1.6 + - - -
333A VAL* 3.1 18.3 + - - +
334A GLN* 4.3 1.9 + - - +
380A ASP* 4.6 3.3 - - - +
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Residues in contact with PRO 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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254A ILE* 3.8 30.0 - - + -
255A GLU 4.3 7.9 - - - +
256A GLU* 3.9 25.6 - - - +
326A ARG 3.3 19.5 - - - +
327A PHE 4.3 8.1 - - - +
328A THR 3.4 18.6 - - - +
330A ALA* 1.4 87.9 - - + +
332A LEU* 1.3 62.8 + - + +
333A VAL 3.3 0.4 + - - -
334A GLN* 4.0 13.9 + - + +
335A THR* 3.9 7.4 + - - -
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Residues in contact with LEU 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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256A GLU* 5.9 0.7 - - - +
257A HIS 4.7 5.4 - - - +
260A CYS* 6.4 1.6 - - + -
328A THR 3.7 14.1 - - - +
329A ALA* 2.9 10.4 + - - +
331A PRO* 1.3 82.0 - - + +
333A VAL* 1.4 65.3 + - - +
334A GLN 3.3 0.7 - - - -
335A THR* 3.2 20.5 - - - +
336A ILE* 3.6 4.9 + - - +
342A ALA* 3.8 18.1 - - + +
343A THR 3.5 24.5 - - - +
344A CYS* 5.1 0.2 - - + -
488A PHE* 3.7 19.9 - - + -
558A ARG* 3.8 36.6 - - + +
559A THR 4.2 4.0 - - - +
560A CYS* 4.0 21.8 - - + +
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Residues in contact with VAL 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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325A TYR* 3.6 23.8 - - - +
329A ALA 3.4 8.0 + - - +
330A ALA 3.1 11.8 + - - +
332A LEU* 1.4 73.1 - - - +
334A GLN* 1.3 63.5 + - - +
336A ILE* 3.3 20.6 - - - +
337A PHE* 3.3 7.3 - - + -
377A ALA* 4.3 13.2 - - + +
380A ASP* 4.2 5.4 - - + -
381A VAL* 3.9 33.9 - - + +
384A LEU* 3.7 20.2 - - + -
488A PHE* 4.1 17.7 - - + -
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Residues in contact with GLN 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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330A ALA 4.3 1.8 + - - +
331A PRO* 4.0 10.4 + - + +
332A LEU 3.3 0.6 - - - -
333A VAL* 1.3 76.8 - - - +
335A THR* 1.4 57.3 + - - +
337A PHE* 2.9 23.3 + - - +
338A GLU* 3.1 26.7 + - + +
384A LEU* 4.1 16.9 - - + +
390A TYR* 4.8 5.7 + - - +
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Residues in contact with THR 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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331A PRO 3.9 4.3 + - - -
332A LEU* 3.2 23.3 + - - -
334A GLN* 1.4 76.5 - - - +
336A ILE* 1.3 55.1 + - - +
338A GLU* 3.2 25.6 + - - +
339A GLY 3.4 0.3 + - - -
340A GLY* 2.8 31.4 + - - -
341A LYS 3.8 18.4 - - - +
342A ALA* 4.5 2.7 - - + -
556A ASN* 3.6 25.8 - - + +
558A ARG* 3.5 27.1 - - + -
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Residues in contact with ILE 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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332A LEU 3.8 11.7 - - - +
333A VAL 3.3 15.5 + - - +
334A GLN 3.3 0.8 - - - -
335A THR* 1.3 75.7 - - - +
337A PHE* 1.3 60.4 + - + +
339A GLY 3.4 4.3 + - - -
340A GLY 3.8 9.4 - - - +
342A ALA* 3.9 8.3 - - + -
381A VAL* 4.3 12.3 - - + -
476A ILE* 4.2 26.2 - - + +
478A LEU* 3.5 27.9 - - + +
485A HIS* 3.3 20.1 - - - -
486A GLY* 3.5 8.7 - - - -
487A LYS 3.4 35.0 - - - +
488A PHE* 3.9 20.0 - - + -
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Residues in contact with PHE 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 VAL* 3.3 22.7 - - + -
334A GLN* 2.9 10.3 + - - +
336A ILE* 1.3 75.2 - - + +
338A GLU* 1.3 54.7 + - - +
339A GLY 3.1 5.2 - - - -
381A VAL* 3.4 40.8 - - + -
384A LEU* 3.6 20.4 - - + -
385A LYS* 3.7 30.7 - - + -
390A TYR* 3.7 52.2 - + + -
395A LEU* 3.9 14.1 - - + -
478A LEU* 3.8 24.9 - - + -
485A HIS* 2.6 23.7 + - - -
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Residues in contact with GLU 338 (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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334A GLN* 3.1 22.9 + - + +
335A THR* 3.2 19.8 + - - +
337A PHE* 1.3 76.2 - - - +
339A GLY* 1.3 60.1 + - - +
340A GLY 4.8 0.2 - - - +
390A TYR* 4.7 10.3 - - - +
485A HIS* 4.2 3.1 - - - -
556A ASN* 4.8 14.5 - - + +
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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