Contacts of the helix formed by residues 526 - 534 (chain B) in PDB entry 4HXG
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 SER 526 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B TRP* 4.0 2.5 - - - -
492B SER 3.3 15.0 - - - -
493B TYR* 3.6 11.6 - - - -
494B TRP* 2.8 25.4 + - - -
522B TYR 2.7 25.1 + - - -
523B ARG 3.4 6.0 + - - +
524B LYS 3.4 2.4 - - - -
525B LEU* 1.3 76.5 - - - +
527B PRO* 1.3 70.2 - - - +
528B LEU 3.0 1.4 + - - -
529B PHE* 3.3 14.5 + - - -
530B TYR* 3.3 12.3 - - - -
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Residues in contact with PRO 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B TYR* 3.3 30.7 - - + -
473B ASN* 3.6 29.6 - - + +
474B TRP* 3.6 39.9 - - + +
477B THR* 3.6 11.7 - - + +
491B ILE 3.9 3.4 - - - +
492B SER* 3.6 10.8 - - - +
494B TRP* 5.4 0.2 - - + -
525B LEU 3.5 1.3 - - - +
526B SER* 1.3 83.1 - - - +
528B LEU* 1.3 62.0 + - - +
529B PHE 3.2 0.2 - - - -
530B TYR* 3.1 14.2 + - + -
531B ALA 3.5 7.3 + - - -
557B PHE* 3.9 6.8 - - + -
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Residues in contact with LEU 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B SER* 2.8 25.0 + - - +
493B TYR* 3.6 35.7 - - + -
526B SER 3.0 0.8 + - - +
527B PRO* 1.3 76.8 - - - +
529B PHE* 1.3 69.9 + - + +
530B TYR 3.5 0.3 + - - -
531B ALA* 3.6 16.1 + - - +
556B MET* 4.0 16.2 - - + +
557B PHE* 3.9 33.2 - - + +
560B VAL* 3.7 34.7 - - + +
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Residues in contact with PHE 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B TYR* 3.6 43.3 - + - -
523B ARG* 3.3 61.0 - - + +
526B SER* 3.3 11.9 + - - +
527B PRO 3.2 0.6 - - - -
528B LEU* 1.3 82.9 - - + +
530B TYR* 1.3 68.8 + - + +
531B ALA 3.4 1.1 + - - -
532B LYS* 5.3 0.7 + - - +
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Residues in contact with TYR 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B TRP* 3.8 10.4 - + - -
477B THR* 3.4 23.8 - - - +
478B GLN* 3.2 25.8 - - - -
523B ARG 4.1 4.7 - - - -
524B LYS* 2.6 41.4 + - - +
526B SER 3.3 21.1 - - - -
527B PRO 3.1 4.1 + - - +
529B PHE* 1.3 84.5 - - + +
531B ALA* 1.3 51.5 + - - +
532B LYS* 3.1 4.0 - - - -
533B ASN* 2.8 49.6 + - - +
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Residues in contact with ALA 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B THR* 4.4 0.7 - - - -
527B PRO 3.5 4.4 + - - -
528B LEU 3.6 14.8 - - - +
529B PHE 3.4 2.0 - - - -
530B TYR* 1.3 77.2 - - - +
532B LYS* 1.3 61.7 + - - +
533B ASN 3.0 1.5 + - - -
534B VAL* 3.2 16.6 + - - -
557B PHE* 4.0 8.5 - - + -
560B VAL* 3.8 10.1 - - + -
561B LEU* 3.7 25.1 - - + +
564B LEU* 3.8 16.8 - - + -
566B LYS* 3.5 14.9 - - - +
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Residues in contact with LYS 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B PHE 5.3 0.6 + - - +
530B TYR 2.9 2.3 + - - +
531B ALA* 1.3 78.2 - - - +
533B ASN* 1.3 63.5 + - - +
535B LYS* 5.9 0.2 - - - +
564B LEU* 3.9 20.8 - - + +
566B LYS* 2.8 23.5 + - - +
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Residues in contact with ASN 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B LEU 3.8 4.7 - - - +
477B THR* 3.1 30.0 + - - +
478B GLN* 4.8 2.2 + - - +
479B SER 5.7 0.2 - - - +
480B ASP* 5.0 5.4 - - - +
530B TYR* 2.8 37.6 + - - +
532B LYS* 1.3 84.3 - - - +
534B VAL* 1.3 61.4 + - - +
535B LYS* 3.2 13.6 + - - +
566B LYS* 4.5 0.2 - - - -
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Residues in contact with VAL 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B LEU* 3.5 40.6 - - + +
477B THR* 3.8 21.5 - - + -
531B ALA 3.2 15.3 + - - +
532B LYS 3.4 0.6 - - - -
533B ASN* 1.3 75.9 - - - +
535B LYS* 1.3 61.2 + - - +
536B ALA 3.5 24.5 - - - +
538B LEU* 5.3 4.3 - - + -
557B PHE* 4.6 7.2 - - + -
561B LEU* 4.2 16.8 - - + -
566B LYS* 3.1 35.1 + - + +
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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