Contacts of the strand formed by residues 482 - 489 (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 GLU 482 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B CYS* 4.0 3.1 - - - -
480B ASP 5.7 1.2 - - - +
481B GLU* 1.3 79.9 - - - +
483B LEU* 1.3 62.3 + - - +
484B LEU* 3.6 19.9 + - + -
507B LEU* 5.8 2.8 - - - +
526B CYS* 3.3 3.6 - - - -
527B CYS* 2.8 36.1 + - - +
529B LEU* 3.9 26.7 - - + +
532B ALA* 4.3 18.7 - - + +
534B CYS* 3.9 23.7 + - - +
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Residues in contact with LEU 483 (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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475B ALA 5.0 0.9 - - - +
477B CYS* 3.7 15.3 - - - -
481B GLU 4.3 0.2 + - - -
482B GLU* 1.3 74.0 + - - +
484B LEU* 1.3 64.6 + - - +
485B SER 3.2 26.0 - - - +
500B MET* 4.1 21.5 - - + +
507B LEU* 3.9 30.4 - - + +
508B VAL* 3.4 39.5 - - - +
509B CYS* 3.8 4.7 - - + +
524B ALA* 3.5 28.3 - - + -
525B ARG 3.6 6.3 - - - +
534B CYS* 5.5 2.8 - - - +
599B SER* 3.9 8.1 + - - -
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU* 5.0 4.9 - - + -
457B CYS* 4.7 0.2 - - - -
482B GLU* 4.1 10.3 - - + +
483B LEU* 1.3 79.8 - - - +
485B SER* 1.3 63.3 + - - +
500B MET* 4.8 0.2 - - - -
525B ARG 2.9 7.6 + - - +
527B CYS* 3.5 40.2 - - + -
529B LEU* 4.4 15.0 - - + -
534B CYS* 3.9 6.5 - - - -
560B THR* 2.7 41.4 + - + +
561B GLY 3.3 2.4 + - - -
599B SER* 3.5 8.0 + - - -
601B CYS* 3.5 31.4 - - - -
606B LEU* 5.5 1.8 - - + -
633B THR* 4.1 25.4 - - + +
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Residues in contact with SER 485 (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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483B LEU* 3.2 13.6 - - - +
484B LEU* 1.3 78.0 - - - +
486B CYS* 1.3 63.1 + - - +
500B MET* 4.1 9.4 - - - -
523B ILE 4.7 0.4 - - - -
525B ARG* 3.1 35.0 + - - +
561B GLY* 3.8 11.7 - - - -
562B CYS 5.0 1.8 - - - -
633B THR 2.6 26.1 + - - -
634B GLY* 3.5 16.2 - - - -
635B CYS 4.4 3.6 + - - -
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Residues in contact with CYS 486 (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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485B SER* 1.3 81.2 + - - +
487B SER* 1.3 59.3 + - - +
498B GLU* 3.3 25.8 - - - +
499B ARG 3.6 13.7 - - - -
500B MET* 3.5 14.6 - - + -
509B CYS* 2.0 53.8 - - + -
510B ARG 3.8 2.2 - - - -
523B ILE 3.5 2.2 - - - -
562B CYS 3.8 7.0 + - - +
563B SER* 2.7 31.3 + - - +
635B CYS 5.4 1.0 - - - +
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Residues in contact with SER 487 (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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486B CYS* 1.3 75.1 - - - +
488B SER* 1.3 64.7 + - - +
498B GLU* 3.6 11.0 - - - +
509B CYS* 3.9 3.8 - - - -
522B ALA* 3.8 2.4 - - - -
523B ILE* 2.9 44.3 + - - +
635B CYS* 3.9 20.3 - - - +
636B SER* 5.8 0.4 - - - -
647B ALA* 2.6 31.1 + - - -
648B TYR* 3.8 5.5 - - - -
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Residues in contact with SER 488 (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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487B SER* 1.3 79.5 - - - +
489B PHE* 1.3 61.2 + - - +
495B ARG* 2.6 26.6 + - - +
497B GLY* 3.7 7.6 - - - -
498B GLU* 2.6 24.7 + - - -
511B ALA* 3.8 18.2 - - - -
520B VAL* 5.3 3.4 - - - -
521B TYR 3.2 14.8 - - - -
523B ILE* 4.0 4.7 - - - -
646B GLY* 3.2 21.3 - - - -
647B ALA 3.2 6.9 + - - -
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Residues in contact with PHE 489 (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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435B VAL* 4.4 17.5 - - + -
461B TRP* 3.9 22.9 - + + -
488B SER* 1.3 78.8 - - - +
490B SER* 1.3 80.1 + - - +
491B ARG* 4.0 26.9 - - + -
495B ARG* 4.8 1.1 - - - -
520B VAL* 3.5 4.6 - - - -
521B TYR* 2.9 42.9 + + - -
523B ILE* 3.8 17.0 - - + +
645B LEU* 3.5 29.8 - - + -
646B GLY* 4.2 3.6 - - - -
648B TYR* 4.3 14.1 - + + -
657B ARG* 4.0 36.6 - - + -
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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