Contacts of the strand formed by residues 465 - 469 (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 ASP 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A GLY* 5.3 1.2 - - - -
424A ARG* 3.4 56.2 + - + +
425A GLY* 6.3 0.4 - - - -
427A ALA* 4.9 2.1 - - - +
463A ASP* 3.0 27.0 + - - +
464A ILE* 1.3 81.1 - - - +
466A THR* 1.3 61.5 + - - +
618A ASP* 2.7 41.2 - - + +
620A LEU* 4.3 1.7 - - + +
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Residues in contact with THR 466 (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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409A TYR* 4.6 9.2 + - - -
410A ILE* 4.1 26.0 - - + +
420A VAL* 4.3 8.5 - - + -
421A GLY 5.3 2.0 - - - +
423A GLY* 6.1 1.8 - - - -
424A ARG* 4.8 1.1 - - - +
438A ILE* 5.3 2.4 - - - +
464A ILE* 4.1 11.8 + - - +
465A ASP* 1.3 76.2 + - - +
467A ASP* 1.3 66.0 - - - +
468A PHE* 3.4 35.9 - - + -
618A ASP 2.9 13.5 + - - +
619A PHE* 3.4 4.9 - - - -
620A LEU* 2.8 32.3 + - - +
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Residues in contact with ASP 467 (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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420A VAL* 3.8 0.2 - - - -
421A GLY* 3.1 31.8 + - - +
422A PRO* 5.9 0.7 - - - +
423A GLY* 4.5 5.8 - - - +
424A ARG* 3.3 26.5 + - - +
466A THR* 1.3 80.1 - - - +
468A PHE* 1.3 69.3 + - - +
620A LEU* 3.3 21.9 - - - +
622A LEU* 4.3 11.7 - - + +
625A LEU* 3.8 14.4 - - + -
821A TYR* 2.7 38.0 + - - -
824A LEU* 5.3 1.4 - - + +
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Residues in contact with PHE 468 (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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409A TYR* 4.2 12.3 - + - -
410A ILE* 4.4 4.5 - - + -
413A ALA* 3.7 21.1 - - + -
418A VAL* 4.0 16.6 - - + -
419A SER 3.4 15.7 - - - +
420A VAL* 3.8 12.3 - - + -
466A THR* 3.4 36.3 - - + -
467A ASP* 1.3 76.2 - - - +
469A SER* 1.3 72.1 + - - +
473A ARG* 4.5 10.3 - - + -
476A VAL* 4.0 22.0 - - + -
619A PHE* 3.7 36.1 - + + -
620A LEU 2.7 10.2 + - - +
621A GLY* 4.4 0.2 - - - -
622A LEU 3.0 20.6 + - - -
625A LEU* 3.4 12.1 - - - +
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Residues in contact with SER 469 (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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418A VAL* 4.8 0.8 - - - +
419A SER* 3.2 28.0 + - - -
468A PHE* 1.3 75.2 - - - +
470A ASP* 1.3 57.8 + - - +
471A ARG* 3.7 6.8 + - - +
472A GLU* 3.1 23.4 + - - +
473A ARG* 2.9 30.0 + - - +
621A GLY* 4.4 0.2 - - - -
625A LEU* 4.0 7.8 - - - +
626A THR* 2.6 31.1 + - - +
629A ASP* 4.5 4.9 + - - -
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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