Contacts of the strand formed by residues 454 - 459 (chain A) in PDB entry 3PQZ
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 LEU 454 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A ILE* 3.3 40.6 - - + +
448A GLN* 3.7 32.1 - - + +
451A VAL* 2.9 31.4 + - + +
452A ASP 3.2 1.0 + - - -
453A GLY* 1.3 77.4 - - - +
455A PHE* 1.3 59.0 + - - +
470A SER 4.0 0.3 - - - +
471A LEU* 3.6 0.5 - - - -
472A CYS* 2.9 29.3 + - + +
525A HIS* 3.3 26.6 + - + +
526A CYS 3.8 7.4 - - - +
527A CYS* 3.7 26.0 - - + +
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Residues in contact with PHE 455 (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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431A TRP* 3.9 32.4 - + + +
445A ILE* 4.9 1.3 - - - -
453A GLY 3.5 8.3 - - - -
454A LEU* 1.3 78.2 - - - +
456A LEU* 1.3 64.9 + - - +
469A LEU* 3.7 19.1 - - + -
470A SER 3.1 11.4 - - - +
471A LEU* 4.0 14.1 - - + -
509A VAL* 3.6 37.0 - - + -
513A GLN* 4.6 8.1 - - - -
523A LEU* 3.9 28.7 - - + -
524A ARG 4.8 0.7 - - - -
525A HIS 2.9 42.8 + - - -
526A CYS* 3.9 5.1 - - + -
527A CYS* 2.8 28.2 + - - +
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Residues in contact with LEU 456 (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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431A TRP 3.3 14.1 - - - +
433A HIS* 3.7 35.0 - - + +
436A ILE* 4.4 3.6 - - + -
441A SER* 4.0 13.2 - - - +
444A LEU* 4.1 10.3 - - + -
445A ILE* 4.2 8.1 - - + -
455A PHE* 1.3 79.4 - - - +
457A VAL* 1.3 71.4 + - - +
458A ARG* 4.0 24.0 - - + -
469A LEU* 3.6 4.9 - - - +
470A SER* 2.9 51.3 + - - +
527A CYS* 3.9 18.2 - - - +
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Residues in contact with VAL 457 (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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431A TRP* 2.7 37.5 + - + -
432A PHE* 3.3 9.8 - - + -
433A HIS* 2.9 27.7 + - - +
455A PHE* 4.7 1.1 - - + -
456A LEU* 1.3 79.9 - - - +
458A ARG* 1.3 70.0 + - - +
467A PHE* 4.3 6.7 - - + -
468A VAL 3.5 9.4 - - - +
469A LEU* 3.8 21.3 - - + -
482A ILE* 4.7 7.4 - - + -
505A LEU* 4.0 28.0 - - + -
508A LEU* 5.8 0.7 - - + -
509A VAL* 4.1 12.1 - - + -
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Residues in contact with ARG 458 (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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432A PHE* 4.2 2.9 - - - -
433A HIS* 4.7 0.7 - - + -
434A GLY 3.2 13.9 - - - +
436A ILE* 3.4 40.8 + - + +
437A SER* 4.5 0.2 - - - +
438A ARG* 3.4 21.0 - - - +
441A SER* 3.3 12.9 + - - -
456A LEU* 4.0 6.5 - - + -
457A VAL* 1.3 77.3 - - - +
459A GLU* 1.3 68.1 + - - +
467A PHE* 3.1 14.3 - - - +
468A VAL* 2.8 53.0 + - + +
470A SER* 3.2 12.9 + - - -
479A HIS* 3.1 24.7 + - - -
3M GLU* 2.8 43.2 + - - -
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Residues in contact with GLU 459 (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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427A ARG* 4.6 12.0 + - - -
432A PHE* 4.4 2.7 - - + -
434A GLY* 2.8 21.5 + - - +
435A ARG* 2.9 55.0 + - + +
436A ILE 4.3 9.2 - - - +
458A ARG* 1.3 86.0 + - - +
460A SER* 1.3 70.9 + - - +
461A GLN* 3.7 0.5 + - - -
464A PRO 4.5 14.4 - - - +
466A GLY 3.9 6.1 - - - +
467A PHE* 3.9 19.5 - - + -
468A VAL 4.8 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