Contacts of the helix formed by residues 479 - 486 (chain A) in PDB entry 4EG8
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 THR 479 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A HIS* 3.8 2.2 - - - -
340A VAL* 3.6 27.8 - - + -
341A VAL* 3.8 27.0 - - + +
344A LEU* 3.3 28.7 - - + +
475A LEU* 2.7 22.6 + - - +
476A ASP 3.4 11.2 - - - -
477A ALA 3.1 0.8 - - - -
478A LEU* 1.3 76.7 - - - +
480A ASN* 1.3 60.9 + - - +
481A TYR 3.1 0.4 - - - -
482A LEU* 2.9 15.5 + - + -
483A THR* 3.0 13.1 + - - +
527A TRP* 4.2 9.3 - - - -
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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
----------------------------------------------------------
246A SER 5.2 0.2 - - - +
248A ILE* 3.4 42.3 - - + +
283A LEU* 3.6 7.8 - - - +
330A ILE* 3.6 19.2 - - + +
332A THR* 4.7 1.1 - - + -
337A HIS* 3.4 21.8 - - + +
477A ALA 2.9 22.8 + - - +
478A LEU 2.9 1.6 + - - -
479A THR* 1.3 76.9 - - - +
481A TYR* 1.3 94.1 + - - +
483A THR* 3.6 1.4 - - - -
484A GLY* 2.9 28.4 + - - -
815A MET* 3.9 1.0 - - - +
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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* 3.5 16.3 - - + -
245A THR* 3.4 26.2 + - + -
246A SER 3.3 20.2 + - - -
247A PRO* 3.7 10.0 - - - +
283A LEU* 4.4 4.7 - - + -
478A LEU* 3.3 18.6 - - + +
479A THR 3.1 0.6 - - - -
480A ASN* 1.3 105.1 - - - +
482A LEU* 1.3 60.6 + - - +
484A GLY* 3.6 0.3 + - - -
485A SER* 3.2 19.2 + - - -
508A PHE* 3.9 5.2 - - + -
513A HIS* 3.4 29.7 - + + +
515A ILE* 4.4 2.6 - - - +
523A HIS* 2.7 42.1 + + - -
527A TRP* 3.9 17.5 - + + -
815A MET* 3.6 15.9 - - + -
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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* 3.7 21.5 - - + +
343A GLU* 5.9 0.4 - - + +
344A LEU* 4.7 15.3 - - + -
478A LEU 4.4 0.4 + - - -
479A THR* 2.9 18.3 + - + +
481A TYR* 1.3 76.9 - - - +
483A THR* 1.3 66.1 + - - +
485A SER* 2.7 23.7 + - - +
486A ARG* 3.4 23.8 + - - +
502A PHE* 4.6 10.8 - - + -
508A PHE* 3.5 39.3 - - + -
527A TRP* 4.4 6.0 - - + -
536A LEU* 4.0 23.8 - - + -
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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* 3.7 17.9 - - + -
334A ASN* 5.3 0.2 - - - +
336A GLN 4.3 0.4 - - - -
337A HIS* 2.9 45.7 + - + +
340A VAL* 3.5 28.8 - - + +
479A THR 3.0 8.3 + - - -
480A ASN 3.6 6.1 - - - -
482A LEU* 1.3 74.2 - - - +
484A GLY* 1.3 59.4 + - - +
486A ARG* 2.8 21.5 + - - +
487A LEU* 3.3 28.8 + - + +
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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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243A PHE* 4.7 0.9 - - - -
281A PHE* 3.5 12.9 - - - -
283A LEU* 4.0 19.5 - - - -
328A TYR* 5.2 0.4 - - - -
330A ILE* 3.9 8.2 - - - +
480A ASN 2.9 16.5 + - - -
481A TYR 4.0 1.8 - - - -
483A THR* 1.3 76.3 - - - +
485A SER* 1.3 58.7 + - - +
486A ARG 3.1 0.5 + - - -
487A LEU* 3.6 10.0 + - - +
507A ARG* 2.9 23.7 + - - -
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Residues in contact with SER 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PHE* 3.9 8.2 - - - -
481A TYR 3.2 13.2 + - - -
482A LEU* 2.7 19.5 + - - +
484A GLY* 1.3 76.2 - - - +
486A ARG* 1.3 64.2 + - - +
487A LEU 3.7 0.7 - - - -
502A PHE* 3.8 7.3 - - - +
505A LEU* 3.5 23.0 - - - +
507A ARG* 3.8 14.6 - - - +
508A PHE* 3.3 44.1 - - - +
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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
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340A VAL* 3.8 24.9 - - - +
343A GLU* 2.9 39.8 + - - -
482A LEU* 3.7 24.8 - - - +
483A THR 2.8 9.7 + - - +
485A SER* 1.3 86.5 - - - +
487A LEU* 1.3 59.9 + - - +
488A ARG 3.9 0.3 + - - -
497A SER 3.6 0.2 - - - +
498A LEU* 3.3 22.7 - - + +
499A VAL* 2.8 62.0 + - + +
500A ASP* 3.3 21.5 + - - +
502A PHE* 3.8 28.7 - - - +
505A LEU* 3.6 5.3 - - - +
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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
------------------------------------------------------------
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