Contacts of the helix formed by residues 472 - 486 (chain A) in PDB entry 4EGA
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 TYR 472 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A TYR* 3.5 15.5 - - - -
368A GLU 2.5 30.9 + - - -
369A SER* 4.0 4.9 - - - -
370A PHE* 3.9 20.8 + + - -
447A LEU* 4.1 19.7 - - + -
448A SER 3.3 20.6 - - - +
449A VAL* 2.7 33.7 + - + +
450A SER* 4.4 2.7 - - - +
451A ARG* 5.2 12.1 - - + -
456A LEU* 5.8 0.9 - - - -
470A CAS 3.3 3.1 + - - -
471A VAL* 1.3 73.2 - - - +
473A VAL* 1.3 79.5 + - + +
474A TRP* 3.0 32.9 + + + -
475A LEU* 3.0 19.3 + - + +
476A ASP* 3.1 9.9 + - - +
522A PHE* 3.8 9.5 - - - -
526A TYR* 4.7 5.1 + + - -
530A PHE* 5.8 1.1 - + - -
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Residues in contact with VAL 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A TYR* 4.2 10.1 - - + +
287A ASP* 3.8 14.4 - - - +
289A HIS* 3.5 36.6 - - + +
290A GLY* 4.0 11.4 - - - -
363A TYR* 4.8 0.2 - - - +
368A GLU* 3.6 40.6 - - + +
456A LEU* 5.6 4.1 - - + +
471A VAL 3.2 5.7 + - - -
472A TYR* 1.3 77.5 - - + +
474A TRP* 1.3 59.8 + - + +
476A ASP* 3.4 7.4 - - - +
477A ALA* 2.7 35.0 + - - +
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Residues in contact with TRP 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A TYR* 3.0 19.0 + + - -
367A ASP 3.4 15.8 + - - -
368A GLU* 3.1 30.9 + - + -
472A TYR* 3.1 24.4 - + + -
473A VAL* 1.3 79.0 - - + +
475A LEU* 1.3 61.1 + - - +
477A ALA* 3.7 3.9 - - + +
478A LEU* 2.8 44.5 + - + +
519A ILE* 3.7 16.8 - - + -
522A PHE* 3.3 59.9 - + + -
523A HIS* 3.8 12.1 - + - -
526A TYR* 5.5 1.1 - - + -
530A PHE* 6.4 0.2 - - + -
550A LYS* 5.2 1.1 - - - -
814A MET* 3.5 49.4 - - + -
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Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A VAL* 5.3 3.8 - - + -
344A LEU* 4.3 13.0 - - + -
345A TRP* 3.9 33.9 - - + -
348A LEU* 4.2 17.9 - - + -
449A VAL* 4.2 16.2 - - + -
471A VAL* 4.1 9.9 - - + -
472A TYR* 3.0 17.8 + - + +
474A TRP* 1.3 73.4 - - - +
476A ASP* 1.3 61.2 + - - +
478A LEU* 4.0 2.4 - - + -
479A THR* 2.7 42.8 + - - +
527A TRP* 5.9 0.4 - - + -
530A PHE* 3.6 42.1 - - + -
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Residues in contact with ASP 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP* 5.2 1.1 - - - -
289A HIS* 2.7 36.5 + - - +
332A THR* 3.7 8.8 - - - -
337A HIS* 2.8 38.1 + - - -
341A VAL* 4.1 11.9 - - - -
461A ILE* 3.5 19.1 + - + +
471A VAL* 4.0 10.7 - - + +
472A TYR 3.1 11.9 + - - +
473A VAL* 3.4 12.4 - - - +
475A LEU* 1.3 75.0 - - - +
477A ALA* 1.3 64.7 + - - +
479A THR* 3.0 12.6 + - - -
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Residues in contact with ALA 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 3.3 9.1 - - + +
287A ASP* 3.0 34.8 - - - +
332A THR* 4.6 0.2 - - - -
473A VAL 2.7 21.9 + - - +
474A TRP* 3.4 10.1 + - + +
476A ASP* 1.3 75.4 + - - +
478A LEU* 1.3 59.5 + - - +
480A ASN* 2.8 33.3 + - - +
814A MET* 3.7 15.0 - - + -
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Residues in contact with LEU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A TRP* 2.8 34.2 + - + +
475A LEU* 4.1 3.6 - - + +
477A ALA* 1.3 71.5 - - - +
479A THR* 1.3 64.9 + - - +
480A ASN 3.0 1.1 + - - -
481A TYR* 3.3 23.5 + - + -
522A PHE* 3.5 30.7 - - + +
523A HIS* 3.7 38.1 - - + +
526A TYR* 4.5 2.7 - - + -
527A TRP* 3.5 38.7 - - + -
530A PHE* 4.0 23.6 - - + -
814A MET* 3.9 7.6 - - + -
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Residues in contact with THR 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A HIS* 3.7 1.3 - - - -
340A VAL* 3.4 30.5 - - + -
341A VAL* 3.9 24.8 - - + +
344A LEU* 3.1 30.3 - - + +
475A LEU* 2.7 19.7 + - - +
476A ASP 3.0 12.5 + - - -
478A LEU* 1.3 76.7 - - - +
480A ASN* 1.3 65.4 + - - +
482A LEU* 2.9 16.4 + - + +
483A THR* 3.0 10.3 + - - +
527A TRP* 4.5 6.2 - - - -
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Residues in contact with ASN 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 3.3 42.6 - - + +
283A LEU* 3.6 13.0 - - - +
330A ILE* 3.7 16.6 - - + +
332A THR* 4.9 1.1 - - + -
337A HIS* 3.4 20.6 - - + -
477A ALA 2.8 24.3 + - - +
478A LEU 3.0 1.4 - - - -
479A THR* 1.3 76.7 - - - +
481A TYR* 1.3 84.8 + - - +
483A THR* 3.6 1.3 - - - -
484A GLY* 2.7 33.1 + - - -
814A MET* 3.7 4.0 - - - +
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Residues in contact with TYR 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PHE* 3.6 11.7 - - + -
245A THR* 3.4 22.8 + - + -
246A SER 3.4 20.2 + - - -
247A PRO* 3.7 9.7 - - - +
283A LEU* 4.3 4.9 - - + -
478A LEU* 3.3 20.4 - - + +
479A THR 3.0 1.0 + - - -
480A ASN* 1.3 104.5 - - - +
482A LEU* 1.3 56.8 + - - +
484A GLY 3.3 0.7 + - - -
485A SER* 3.0 27.9 + - - -
508A PHE* 4.1 5.4 - - + -
513A HIS* 3.4 29.2 - + + -
515A ILE* 4.5 2.6 - - - +
523A HIS* 2.8 40.0 + + - -
527A TRP* 4.0 17.3 - + + -
814A MET* 3.4 19.1 - - + +
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Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A VAL* 3.8 12.8 - - + -
344A LEU* 4.4 14.8 - - + -
479A THR* 2.9 9.9 + - + +
481A TYR* 1.3 75.3 - - - +
483A THR* 1.3 65.5 + - - +
485A SER* 2.6 28.1 + - - +
486A ARG* 3.3 17.8 + - - +
502A PHE* 4.5 7.6 - - + -
508A PHE* 3.6 32.6 - - + -
527A TRP* 4.4 8.8 - - + -
536A LEU* 3.8 18.4 - - + -
806A GOL 3.5 42.4 - - - +
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Residues in contact with THR 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ILE* 3.5 18.6 - - + -
334A ASN* 5.7 0.2 - - - +
336A GLN 4.4 1.6 - - - -
337A HIS* 3.2 43.5 + - + +
340A VAL* 3.2 34.8 - - + +
479A THR* 3.0 7.7 + - - +
480A ASN 3.6 7.0 - - - -
482A LEU* 1.3 74.6 - - - +
484A GLY* 1.3 64.9 + - - +
486A ARG* 3.1 12.7 + - - +
487A LEU* 3.3 25.3 + - + +
498A LEU* 4.8 0.2 - - + -
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Residues in contact with GLY 484 (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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281A PHE* 3.7 10.0 - - - -
283A LEU* 3.8 21.5 - - - -
328A TYR* 5.3 0.4 - - - -
330A ILE* 3.9 7.4 - - - +
480A ASN 2.7 21.9 + - - -
481A TYR 3.7 1.8 - - - -
483A THR* 1.3 73.8 - - - +
485A SER* 1.3 59.3 + - - +
486A ARG 3.0 1.0 + - - -
487A LEU* 3.3 11.7 + - - +
507A ARG* 2.9 21.8 + - - -
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Residues in contact with SER 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PHE* 3.9 10.9 - - - -
481A TYR 3.0 13.2 + - - -
482A LEU* 2.6 22.2 + - - +
484A GLY* 1.3 75.7 - - - +
486A ARG* 1.3 56.4 + - - +
487A LEU 3.6 0.2 - - - -
502A PHE* 4.0 8.7 - - - +
505A LEU* 3.5 24.6 - - - +
507A ARG* 3.7 16.9 + - - +
508A PHE* 3.3 43.8 - - - +
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A VAL* 3.9 13.6 - - - +
343A GLU* 2.9 28.9 + - - -
482A LEU* 3.7 22.7 - - - +
483A THR 3.1 3.0 + - - +
484A GLY 3.0 0.8 - - - -
485A SER* 1.3 77.7 + - - +
487A LEU* 1.3 59.9 + - - +
488A ARG 3.8 0.2 + - - -
497A SER 3.7 0.2 - - - +
498A LEU* 3.5 25.5 - - + +
499A VAL* 2.6 65.4 + - + +
500A ASP* 3.4 20.1 + - - +
502A PHE* 3.7 35.2 - - + +
505A LEU* 3.5 5.6 - - - +
806A GOL 2.8 37.2 + - - -
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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