Contacts of the strand formed by residues 522 - 528 (chain A) in PDB entry 1ASZ
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 HIS 522 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A GLN* 3.5 15.0 + - + +
310A ILE* 3.4 21.3 - - + +
344A GLU* 3.3 29.2 - - + -
345A MET 2.7 25.1 - - - +
346A ALA* 3.7 3.8 - - - +
347A PHE* 3.8 5.9 - - - -
484A GLN* 3.7 5.2 - - - +
485A ARG* 3.1 57.3 + - + +
487A HIS* 4.0 14.4 - - + -
515A PHE* 4.3 8.1 - + - -
519A CYS* 3.7 19.3 - - - -
520A PRO 2.9 19.4 + - - -
521A PRO* 1.3 73.2 - - - +
523A ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 523 (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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344A GLU* 3.6 7.0 - - - -
345A MET* 2.7 36.3 + - - +
347A PHE* 4.1 8.0 - - + -
351A TYR* 4.4 5.6 - - + +
354A VAL* 3.6 27.3 - - + +
470A TYR* 4.4 1.3 - - - +
483A ALA 2.7 25.1 - - - +
484A GLN* 3.8 5.8 - - + +
485A ARG* 4.7 3.1 - - - +
522A HIS* 1.3 75.8 - - - +
524A GLY* 1.3 53.6 + - - +
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Residues in contact with GLY 524 (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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343A MET* 3.8 17.7 - - - -
344A GLU* 3.3 12.3 + - - -
354A VAL* 4.1 2.7 - - - -
358A LEU* 4.3 2.9 - - - -
470A TYR* 2.9 9.4 + - - -
482A GLY* 2.9 2.6 - - - -
483A ALA 2.8 27.3 + - - -
485A ARG* 3.4 8.4 + - - +
523A ALA* 1.3 77.9 - - - +
525A GLY* 1.3 57.9 + - - -
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Residues in contact with GLY 525 (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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306A LYS* 4.9 4.5 - - - -
341A LEU 4.2 0.7 - - - +
342A ASP* 3.9 1.0 - - - -
343A MET* 3.6 34.3 + - - +
358A LEU* 4.3 3.1 - - - +
480A LEU* 4.4 9.6 - - - +
481A SER 3.0 15.0 - - - -
482A GLY* 3.5 3.4 - - - -
485A ARG* 3.8 6.6 - - - +
524A GLY* 1.3 75.4 - - - -
526A GLY* 1.3 59.6 - - - -
527A ILE* 4.2 2.1 + - - +
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Residues in contact with GLY 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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341A LEU 3.5 7.4 - - - -
342A ASP* 4.0 15.2 + - - -
480A LEU* 3.3 13.7 - - - -
481A SER 2.9 12.0 + - - -
525A GLY* 1.3 74.8 - - - -
527A ILE* 1.3 62.7 + - - -
701A ATP 3.1 29.8 - - - +
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Residues in contact with ILE 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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258A PHE* 3.8 33.0 - - + -
338A PHE* 5.1 0.5 - - - -
340A GLY* 3.4 4.5 - - - -
341A LEU* 2.8 46.7 + - + +
342A ASP* 5.0 0.2 - - - +
343A MET* 6.4 0.7 - - + -
358A LEU* 5.7 1.8 - - + -
361A LEU* 4.2 9.6 - - + -
362A PHE* 3.8 22.9 - - + -
365A ILE* 5.6 2.5 - - + -
479A ILE 3.3 11.0 - - - +
480A LEU* 4.0 18.4 - - + -
525A GLY 5.2 1.8 - - - +
526A GLY* 1.3 77.0 - - - -
528A GLY* 1.3 65.2 + - - +
529A LEU 4.0 0.2 - - - -
532A VAL* 3.4 30.7 - - + -
701A ATP 4.1 2.8 - - - +
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Residues in contact with GLY 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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338A PHE* 4.4 9.9 - - - -
339A THR 4.3 2.9 - - - -
479A ILE* 3.5 7.9 + - - +
527A ILE* 1.3 75.0 - - - +
529A LEU* 1.3 65.5 + - - -
530A GLU 3.3 2.5 - - - -
531A ARG* 3.3 7.2 + - - +
532A VAL* 3.2 23.4 + - - +
701A ATP 3.8 26.3 + - - -
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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
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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