Contacts of the helix formed by residues 525 - 535 (chain X) in PDB entry 6AH0
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 525 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474X LEU* 6.0 0.2 - - - -
475X ALA 3.3 12.3 - - - -
476X PRO 5.5 2.7 - - - -
477X THR 5.7 4.7 - - - -
478X ARG* 6.0 1.8 - - - +
502X VAL 3.3 8.5 + - - -
503X ILE* 4.7 5.8 - - - +
524X ALA* 1.3 76.3 - - - +
526X PRO* 1.3 65.4 - - - +
527X GLY 3.4 2.5 - - - -
528X ARG* 3.3 5.6 + - - +
529X LEU* 2.9 21.1 + - - -
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Residues in contact with PRO 526 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474X LEU* 6.1 0.6 - - - -
475X ALA 4.0 5.7 - - - -
476X PRO* 5.6 1.4 - - - -
524X ALA 4.5 0.2 - - - -
525X THR* 1.3 70.6 - - - +
527X GLY* 1.3 61.5 + - - +
529X LEU* 3.4 1.2 + - - -
530X ILE* 3.1 21.3 + - - -
562X ASP* 5.4 12.7 - - - +
563X VAL* 6.0 2.0 - - - +
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Residues in contact with GLY 527 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525X THR 3.4 0.8 - - - -
526X PRO* 1.3 77.1 - - - +
528X ARG* 1.3 60.7 + - - +
530X ILE* 4.3 0.3 - - - -
531X ASP* 3.4 17.5 + - - -
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Residues in contact with ARG 528 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502X VAL 4.9 10.8 - - - -
503X ILE* 5.6 5.8 - - - +
525X THR* 3.3 6.5 + - - +
526X PRO 3.3 0.2 - - - -
527X GLY* 1.3 76.8 - - - +
529X LEU* 1.3 62.5 + - - +
531X ASP* 3.4 2.1 + - - -
532X VAL* 3.2 18.7 + - - -
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Residues in contact with LEU 529 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502X VAL 4.7 4.1 + - - -
524X ALA* 6.0 2.0 - - - +
525X THR 2.9 16.8 + - - -
526X PRO* 3.9 1.3 - - - -
528X ARG* 1.3 75.2 - - - +
530X ILE* 1.3 64.4 + - - +
532X VAL* 3.3 1.9 + - - +
533X LEU* 3.0 20.3 + - - -
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Residues in contact with ILE 530 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526X PRO 3.1 15.8 + - - -
527X GLY 4.3 0.9 - - - -
529X LEU* 1.3 76.3 - - - +
531X ASP* 1.3 52.5 + - - +
533X LEU* 3.2 1.3 + - - +
534X GLU* 2.7 34.1 + - - -
562X ASP 6.0 1.8 - - - -
566X ILE* 5.9 8.1 - - - +
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Residues in contact with ASP 531 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527X GLY 3.4 13.9 + - - -
528X ARG 3.4 3.5 + - - -
529X LEU 3.3 0.2 - - - -
530X ILE* 1.3 75.6 - - - +
532X VAL* 1.3 61.6 + - - +
534X GLU* 3.4 1.9 + - - +
535X ASN* 3.1 19.2 + - - -
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Residues in contact with VAL 532 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528X ARG 3.2 14.3 + - - -
529X LEU* 3.8 3.4 - - - +
530X ILE 3.2 0.2 - - - -
531X ASP* 1.3 75.6 - - - +
533X LEU* 1.3 62.1 + - - +
535X ASN* 3.4 1.4 + - - +
536X ARG 3.1 2.8 + - - -
537X TYR* 2.9 33.4 + - - +
538X LEU* 3.8 5.2 + - - -
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Residues in contact with LEU 533 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529X LEU 3.0 14.9 + - - -
530X ILE* 3.7 2.7 - - - +
532X VAL* 1.3 73.6 - - - +
534X GLU* 1.3 61.1 + - - +
536X ARG* 2.9 19.2 + - - -
538X LEU 4.1 13.1 - - - +
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Residues in contact with GLU 534 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530X ILE 2.7 20.6 + - - -
531X ASP* 3.8 3.1 - - - +
533X LEU* 1.3 73.1 - - - +
535X ASN* 1.3 57.5 + - - +
536X ARG 3.8 0.2 + - - -
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Residues in contact with ASN 535 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531X ASP 3.1 13.3 + - - -
532X VAL 3.4 2.0 + - - -
533X LEU 3.1 0.6 - - - -
534X GLU* 1.3 76.8 - - - +
536X ARG* 1.3 65.3 + - - +
537X TYR* 3.1 4.8 + - - -
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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