Contacts of the strand formed by residues 506 - 513 (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 LYS 506 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B CYS 6.1 0.7 - - - +
478B ALA 5.6 2.0 - - - +
479B PRO* 3.8 34.7 + - + +
481B GLU 5.7 3.8 - - - +
502B ALA* 4.0 2.0 - - - -
503B GLN 2.7 36.7 + - - +
504B GLY 3.4 5.1 - - - +
505B GLY* 1.3 86.6 + - - +
507B LEU* 1.3 67.9 + - - +
508B VAL* 3.6 6.7 + - + +
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Residues in contact with LEU 507 (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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477B CYS* 5.2 7.4 + - - +
482B GLU* 5.8 2.5 - - - +
483B LEU* 3.9 37.1 - - + +
500B MET* 4.8 1.6 - - + +
501B GLU* 3.0 28.5 - - - +
502B ALA* 3.8 11.4 - - + +
505B GLY 4.2 0.2 - - - -
506B LYS* 1.3 77.7 - - - +
508B VAL* 1.3 62.4 + - - +
534B CYS* 5.1 7.9 - - + +
535B SER* 4.6 17.0 - - - +
536B VAL* 3.9 33.0 - - + +
599B SER* 5.9 2.0 - - - +
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Residues in contact with VAL 508 (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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474B VAL* 4.0 20.9 - - + -
475B ALA 4.0 5.8 - - - +
476B ARG* 4.0 26.5 - - + +
483B LEU* 3.4 10.4 - - - +
499B ARG 3.8 0.2 - - - +
500B MET* 3.3 6.2 - - - -
501B GLU* 2.5 46.7 + - + +
503B GLN* 4.1 31.4 - - + +
506B LYS* 3.7 12.6 - - + +
507B LEU* 1.3 77.8 - - - +
509B CYS* 1.3 64.4 + - - +
510B ARG* 4.7 4.9 - - + -
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Residues in contact with CYS 509 (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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473B ALA 3.6 0.9 - - - +
474B VAL* 3.2 5.9 - - - +
475B ALA* 2.8 43.5 + - + +
483B LEU* 3.8 4.2 - - + +
486B CYS* 2.0 57.0 - - + -
487B SER 3.9 2.9 - - - -
508B VAL* 1.3 74.5 - - - +
510B ARG* 1.3 57.9 + - - +
522B ALA* 3.6 4.5 - - - +
523B ILE 3.6 26.7 - - - -
524B ALA* 4.0 13.7 - - + -
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Residues in contact with ARG 510 (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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472B THR* 3.8 36.6 + - + +
473B ALA 3.3 4.7 - - - +
474B VAL* 4.2 12.9 - - + +
498B GLU* 3.2 3.5 - - - -
499B ARG* 2.7 63.4 + - + +
501B GLU* 2.9 27.3 + - + +
503B GLN* 4.5 14.8 - - - +
508B VAL* 4.7 8.5 - - + -
509B CYS* 1.3 75.5 - - - +
511B ALA* 1.3 60.4 + - - +
512B HIS* 3.4 29.6 - - - +
522B ALA* 4.5 0.2 - - - -
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Residues in contact with ALA 511 (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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472B THR* 3.1 10.4 - - - -
473B ALA* 2.8 28.8 + - + +
488B SER* 3.8 10.3 - - - -
497B GLY 3.4 10.5 - - - +
498B GLU* 4.0 2.2 - - + +
510B ARG* 1.3 74.8 - - - +
512B HIS* 1.3 63.5 + - - +
520B VAL* 3.9 13.2 - - + +
521B TYR 3.8 14.8 - - - +
522B ALA* 3.7 22.4 - - + +
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Residues in contact with HIS 512 (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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470B MET* 6.4 0.6 - - - +
471B ALA 3.9 2.4 + - - +
472B THR* 3.4 19.5 - - + +
495B ARG 3.9 0.5 - - - -
496B ARG* 2.9 66.3 + - + +
497B GLY 2.9 11.9 + - - +
499B ARG* 3.2 38.1 + - - -
510B ARG* 3.4 31.9 + - + +
511B ALA* 1.3 76.5 - - - +
513B ASN* 1.3 59.9 - - - +
520B VAL* 3.7 9.6 - - - +
565B HIS* 4.2 24.8 - + + -
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Residues in contact with ASN 513 (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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465B SER* 4.1 12.1 - - - +
466B GLY 3.3 17.2 + - - -
467B PRO 3.6 1.6 + - - -
468B THR 3.6 14.5 + - - +
469B ARG 4.3 5.9 - - - +
471B ALA* 3.3 22.5 + - + +
494B LYS 3.6 10.6 - - - +
496B ARG* 3.7 20.2 + - - -
512B HIS* 1.3 75.3 - - - +
514B ALA* 1.3 79.1 + - - +
515B PHE 3.7 0.9 + - - -
517B GLY 3.2 23.0 + - - -
519B GLY* 3.2 23.9 + - - +
520B VAL* 3.7 8.2 - - - +
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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