Contacts of the strand formed by residues 521 - 528 (chain B) in PDB entry 2PMW
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 TYR 521 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B ARG* 5.2 2.2 - - - -
435B VAL* 5.9 0.4 - - + -
436B LEU* 3.9 28.0 - - + +
461B TRP* 3.6 37.0 - + + -
462B SER* 3.4 23.6 - - - +
463B ALA* 5.1 0.2 - - - -
464B HIS* 3.5 40.8 - + + +
488B SER* 3.2 11.4 - - - -
489B PHE* 2.9 47.4 + + - +
490B SER* 5.4 1.1 - - - -
491B ARG* 2.9 43.2 + - + -
511B ALA* 3.8 3.3 - - - +
520B VAL* 1.3 74.8 - - - +
522B ALA* 1.3 61.1 + - - +
523B ILE* 4.5 0.4 - - + -
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Residues in contact with ALA 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B SER* 2.8 39.1 + - - +
473B ALA* 3.3 29.5 - - - +
475B ALA* 3.7 8.2 - - - +
487B SER 3.8 2.5 - - - -
509B CYS* 3.6 21.1 - - - +
511B ALA* 3.7 13.7 - - + +
521B TYR* 1.3 74.2 - - - +
523B ILE* 1.3 62.9 + - - +
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Residues in contact with ILE 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B THR* 3.5 31.6 - - + -
460B VAL 3.4 4.7 - - - +
461B TRP* 3.5 45.1 - - + +
486B CYS* 3.5 4.0 - - - -
487B SER* 2.9 43.8 + - - +
488B SER 4.0 7.4 - - - -
489B PHE* 3.8 15.5 - - + +
509B CYS* 3.8 2.6 - - - -
521B TYR 4.3 1.3 - - - +
522B ALA* 1.3 80.4 - - - +
524B ALA* 1.3 58.8 + - - +
525B ARG 4.1 0.2 + - - -
647B ALA 3.6 20.9 - - - +
648B TYR* 3.8 11.2 - - + -
649B ALA 5.1 1.1 - - - +
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Residues in contact with ALA 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B ARG 3.7 0.3 - - - +
459B THR* 3.4 6.9 - - - +
460B VAL* 2.8 38.3 + - + +
475B ALA* 3.5 28.8 - - + +
483B LEU* 3.5 20.2 - - + -
485B SER 3.8 4.9 - - - -
509B CYS* 4.0 3.6 - - + -
523B ILE* 1.3 74.5 - - - +
525B ARG* 1.3 59.5 + - - +
526B CYS* 3.9 14.4 - - - -
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Residues in contact with ARG 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B CYS* 3.6 28.0 + - + +
458B ARG* 3.5 16.8 - - - +
459B THR* 2.7 34.3 + - - +
482B GLU 3.7 0.2 - - - +
483B LEU* 3.6 3.5 - - - +
484B LEU* 2.9 29.1 + - - +
485B SER* 3.1 30.4 + - - +
523B ILE 4.1 0.2 + - - -
524B ALA* 1.3 73.4 - - - +
526B CYS* 1.3 59.9 + - - +
527B CYS* 4.4 2.7 - - - -
631B THR* 4.2 2.2 - - - +
632B LEU* 2.8 27.3 + - - +
633B THR* 3.3 21.8 - - - +
649B ALA* 3.9 15.7 - - - +
651B ASP* 2.8 34.2 + - - +
652B ASN* 3.8 10.5 + - - -
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Residues in contact with CYS 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B GLN* 3.0 10.3 + - - -
458B ARG* 2.9 43.6 + - + +
460B VAL* 3.8 18.4 - - - -
477B CYS* 2.0 53.2 - - + -
481B GLU* 3.5 17.7 - - - +
482B GLU 3.3 4.0 - - - -
524B ALA* 3.9 10.5 - - - -
525B ARG* 1.3 74.3 - - - +
527B CYS* 1.3 61.7 + - - +
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Residues in contact with CYS 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B GLN* 4.1 0.4 - - - +
455B LEU* 4.0 7.4 - - + -
456B PHE 3.1 7.0 - - - +
457B CYS* 2.0 47.3 - - - -
481B GLU* 3.3 7.0 - - - +
482B GLU* 2.8 32.4 + - - +
484B LEU* 3.5 39.5 - - + -
525B ARG* 4.3 6.3 - - - -
526B CYS* 1.3 75.2 - - - +
528B LEU* 1.3 65.1 + - - +
529B LEU* 3.5 3.6 + - + +
633B THR* 4.9 0.2 - - - -
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Residues in contact with LEU 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B ALA* 4.7 2.9 - - + -
410B GLU* 3.9 35.2 - - + -
413B GLN* 3.8 31.4 - - + +
414B ARG* 4.3 3.4 - - - +
453B TRP* 3.3 21.4 - - + +
454B GLN 4.8 0.4 - - - +
455B LEU* 3.9 7.6 - - - +
456B PHE* 3.0 32.9 + - + +
480B ASP* 3.9 18.8 - - - +
481B GLU* 3.6 26.9 - - + +
527B CYS* 1.3 70.3 - - - +
529B LEU* 1.3 60.1 + - - +
530B PRO* 3.9 5.4 - - + -
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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