Contacts of the strand formed by residues 574 - 581 (chain A) in PDB entry 4IQJ
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 VAL 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A GLN* 4.0 17.7 - - + +
492A ILE 3.7 10.1 - - - +
493A GLY* 4.1 0.2 - - - -
494A THR* 3.3 15.2 + - - -
573A SER* 1.3 91.5 + - - +
575A HIS* 1.3 83.1 + - - +
576A ALA 3.9 1.0 + - - -
595A ASP* 3.9 22.0 - - + +
599A ARG* 4.9 7.4 - - - -
601A VAL* 3.6 31.6 - - + -
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Residues in contact with HIS 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLN* 3.6 15.9 + - - -
492A ILE* 2.7 23.1 + - + +
493A GLY 4.6 0.7 - - - +
494A THR* 2.6 29.6 + - + +
574A VAL* 1.3 83.2 - - - +
576A ALA* 1.3 73.0 + - + +
577A ALA* 3.2 10.6 + - + +
578A GLY* 3.4 25.4 + - - +
606A MET* 3.2 41.9 - - + +
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Residues in contact with ALA 576 (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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473A ARG* 2.9 34.1 + - - +
491A GLN* 4.5 0.3 + - - -
574A VAL 3.9 2.4 + - - -
575A HIS* 1.3 80.8 + - + +
577A ALA* 1.3 61.3 + - + +
619A PHE 3.9 1.2 - - - +
620A LEU* 6.5 0.2 - - - -
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Residues in contact with ALA 577 (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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473A ARG* 4.3 1.1 - - - +
575A HIS* 3.8 8.0 - - + +
576A ALA* 1.3 78.8 - - + +
578A GLY* 1.3 65.5 + - - +
579A VAL* 3.2 9.7 + - - +
617A MET 3.3 0.2 - - - +
618A ASP* 3.3 15.6 - - + +
619A PHE 3.1 45.8 + - - +
620A LEU* 3.9 20.0 - - + -
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Residues in contact with GLY 578 (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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491A GLN* 3.2 27.0 + - - +
492A ILE* 3.3 16.6 + - - -
575A HIS* 3.4 30.9 + - - +
577A ALA* 1.3 74.9 - - - +
579A VAL* 1.3 66.1 + - - +
606A MET* 4.3 2.7 - - - -
617A MET 4.1 3.4 - - - -
618A ASP* 4.2 3.6 - - - -
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Residues in contact with VAL 579 (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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477A ILE* 4.0 24.5 - - + -
480A VAL* 5.2 2.9 - - + -
489A VAL* 4.2 16.8 - - + -
490A ALA 4.0 6.3 - - - +
491A GLN* 4.2 3.6 - - + +
492A ILE* 4.3 2.0 - - - +
577A ALA 3.6 10.1 - - - +
578A GLY* 1.3 80.0 - - - +
580A VAL* 1.3 75.3 + - - +
581A ILE* 4.7 7.0 - - + -
616A LYS* 3.5 5.7 - - - +
617A MET* 2.9 39.7 + - + +
619A PHE* 3.8 37.2 - - + -
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Residues in contact with VAL 580 (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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488A LYS 4.3 0.2 - - - -
489A VAL* 3.4 25.6 - - - +
490A ALA 2.9 18.4 + - - +
492A ILE* 3.3 35.9 - - + -
579A VAL* 1.3 74.3 - - - +
581A ILE* 1.3 70.0 + - - +
582A ALA 4.0 2.9 - - - +
586A LEU* 4.0 24.9 - - + -
602A THR* 4.0 10.3 - - + +
609A VAL* 3.9 22.2 - - + -
614A LEU* 4.5 10.5 - - + -
615A LEU 3.7 11.9 - - - +
616A LYS* 5.1 0.4 - - + -
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Residues in contact with ILE 581 (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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296A PRO* 3.5 34.2 - - + +
405A ILE* 4.3 18.6 - - + -
409A TYR* 4.8 4.9 - - + -
480A VAL* 3.4 31.2 - - + -
484A TYR* 4.2 28.0 - - + -
488A LYS 3.8 2.7 - - - -
489A VAL* 4.2 3.6 - - + -
579A VAL* 4.3 5.4 + - + -
580A VAL* 1.3 79.0 - - - +
582A ALA* 1.3 64.3 + - - +
615A LEU* 3.2 32.1 + - + +
617A MET* 4.2 22.9 - - + -
619A PHE* 5.6 0.4 - - + -
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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