Contacts of the helix formed by residues 525 - 530 (chain A) in PDB entry 5AM1
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 TRP 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A PHE 3.9 8.1 - - - -
268A PRO* 3.8 14.8 - - + -
269A GLU* 3.3 32.8 - - + -
334A HIS* 4.5 3.6 - - - -
408A LEU* 2.8 37.8 + - + -
409A PHE* 3.4 33.0 - + - -
410A ARG 3.5 28.0 + - - -
441A MET* 3.9 8.7 - - + -
523A GLY* 3.5 1.2 - - - -
524A HIS* 1.3 94.5 - + + +
526A THR* 1.4 62.1 + - - +
527A GLN* 3.2 5.9 + - - -
528A MET* 3.3 23.1 + - + -
529A ASP* 3.0 24.4 + - - +
1548A SO4 3.3 29.3 + - - -
1552A I5T 4.4 5.2 - + - -
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Residues in contact with THR 526 (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 HIS* 3.7 3.5 + - - -
358A LEU* 4.2 12.3 - - + -
359A ASN* 2.5 41.7 + - - +
491A VAL* 5.3 2.7 - - + -
492A THR 6.3 0.2 - - - -
493A ALA* 4.1 3.2 - - + +
519A ILE* 4.2 9.4 - - + -
522A CYS* 3.8 22.3 - - - -
523A GLY 3.7 3.2 + - - -
524A HIS 3.0 2.7 + - - -
525A TRP* 1.4 72.2 - - - +
527A GLN* 1.4 63.8 + - - +
530A LYS* 3.1 25.1 + - - -
534A VAL* 3.5 26.2 - - + +
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Residues in contact with GLN 527 (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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265A HIS* 5.1 2.0 - - - +
269A GLU* 4.6 2.0 + - - +
273A SER* 3.2 30.5 + - - +
274A TRP* 3.6 35.1 - - + +
276A TYR* 4.1 3.5 - - - -
277A GLN* 3.2 32.3 + - - +
334A HIS* 3.3 52.3 + - - +
358A LEU* 3.9 9.0 - - + -
525A TRP 3.2 1.6 + - - -
526A THR* 1.4 72.5 + - - +
528A MET* 1.3 57.3 + - - +
531A PRO* 3.2 29.8 - - - +
534A VAL* 4.2 3.8 - - - -
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Residues in contact with MET 528 (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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228A LEU* 5.7 1.7 - - - +
269A GLU* 4.6 6.7 - - - +
273A SER* 4.7 4.9 - - - +
275A ARG* 3.6 21.8 - - - +
276A TYR* 4.3 11.9 - - + -
409A PHE* 3.8 35.0 - - + -
441A MET* 4.0 33.2 - - + +
442A VAL* 3.6 28.3 - - - -
450A TYR* 4.2 16.2 - - + +
525A TRP* 3.5 30.5 - - + +
527A GLN* 1.3 76.5 - - + +
529A ASP* 1.4 63.5 + - - +
530A LYS 3.6 0.2 - - - -
531A PRO* 3.4 11.4 - - - +
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Residues in contact with ASP 529 (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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410A ARG 5.3 0.2 - - - +
411A ALA* 4.2 10.3 - - - +
412A SER* 4.4 1.2 + - - -
440A ARG* 3.6 15.0 + - - -
441A MET* 3.5 22.8 - - - +
521A ASP 3.8 4.7 - - - +
522A CYS* 4.1 8.3 - - - -
523A GLY* 2.7 34.0 + - - -
525A TRP* 3.0 21.5 + - - +
526A THR 4.0 2.9 - - - +
528A MET* 1.4 79.6 - - - +
530A LYS* 1.3 85.9 + - - +
531A PRO* 3.5 3.9 - - - +
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Residues in contact with LYS 530 (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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440A ARG* 3.9 16.8 - - - +
519A ILE* 3.7 22.0 - - + -
520A GLU 4.1 7.6 - - - +
521A ASP* 3.4 24.7 + - - -
522A CYS* 3.9 13.5 - - + -
526A THR 3.1 8.9 + - - +
529A ASP* 1.3 103.9 + - - +
531A PRO* 1.4 64.0 - - - +
532A THR 3.4 2.2 - - - -
533A GLU* 3.4 36.2 + - + +
534A VAL* 3.1 22.0 + - - +
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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