Contacts of the strand formed by residues 516 - 523 (chain B) in PDB entry 2D2O
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 516 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B ALA* 3.3 2.8 - - - +
509B HIS* 3.9 15.3 + - + +
510B ALA* 3.5 2.1 - - - -
511B ASP* 3.0 27.3 + - + -
514B ALA* 3.0 43.2 - - + +
515B ASN* 1.3 79.5 - - - +
517B TYR* 1.3 60.0 + - - +
531B VAL* 5.0 10.5 - - + -
532B LEU 3.4 4.7 - - - +
533B ASN* 3.2 25.1 - - + +
539B GLN* 3.0 29.2 - - + +
541B VAL* 3.8 37.2 - - + +
573B LEU* 5.1 4.5 - - + -
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Residues in contact with TYR 517 (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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383B PHE* 4.3 13.0 - - + -
391B ALA* 4.0 16.6 - - + -
394B PHE* 3.9 16.8 - + - -
395B ASP* 3.7 42.1 + - + -
398B LEU* 3.9 17.0 - - + +
442B PHE* 4.0 12.8 - + - -
446B TYR* 4.5 6.2 - - - -
505B VAL* 5.4 0.5 - - - +
507B SER* 4.6 5.3 + - - -
509B HIS* 3.3 9.2 - - - -
510B ALA* 4.4 0.9 - - + -
515B ASN 4.1 0.6 + - - -
516B LEU* 1.3 76.1 - - - +
518B ALA* 1.3 66.9 + - - +
519B PHE* 3.3 43.6 - + + +
531B VAL* 5.2 0.9 - - - -
532B LEU* 2.8 53.5 + - + +
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Residues in contact with ALA 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B TRP* 2.7 50.1 + - + -
509B HIS* 2.7 28.8 + - + +
517B TYR* 1.3 84.2 - - - +
519B PHE* 1.3 57.9 + - - +
530B VAL 3.1 14.1 - - - +
531B VAL* 3.9 16.2 - - + -
543B LEU* 4.3 1.8 - - + -
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Residues in contact with PHE 519 (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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442B PHE* 3.8 22.9 - + - -
445B THR* 3.4 45.1 - - - -
446B TYR* 4.1 10.5 - + - -
505B VAL* 3.7 22.4 - - + -
506B ARG 3.3 14.8 - - - +
507B SER* 4.5 0.2 - - - -
508B TRP* 3.7 3.3 - - - -
517B TYR* 3.3 34.5 - + - +
518B ALA* 1.3 75.3 - - - +
520B VAL* 1.3 65.4 + - - +
521B ARG* 3.9 12.8 - - + -
529B GLY* 3.5 1.9 - - - -
530B VAL* 2.9 59.4 + - + +
532B LEU* 4.9 1.8 - - + -
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Residues in contact with VAL 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B ASN* 3.9 1.4 + - - +
505B VAL* 3.4 4.5 - - - -
506B ARG* 2.8 39.6 + - + +
507B SER 5.5 0.7 - - - +
508B TRP* 3.7 32.8 - - + -
519B PHE* 1.3 78.6 - - - +
521B ARG* 1.3 69.6 + - - +
522B THR* 3.5 20.4 + - - +
527B HIS* 4.1 12.6 - - + +
528B VAL 3.4 12.8 - - - +
529B GLY* 4.3 3.6 - - - +
546B PRO* 3.7 23.3 - - + -
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Residues in contact with ARG 521 (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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411B GLN* 3.8 4.4 - - - +
445B THR 2.9 32.8 + - - +
446B TYR 3.4 8.3 + - - -
447B LEU* 3.6 22.3 - - - +
448B GLY 5.0 0.4 - - - +
499B SER* 3.2 35.0 + - - +
500B LEU* 2.9 37.7 + - + +
501B THR 4.2 0.4 - - - -
503B GLY 2.8 23.2 + - - +
504B ASN 2.9 20.7 + - - -
505B VAL* 3.7 23.7 - - - +
519B PHE* 3.9 11.7 - - + -
520B VAL* 1.3 69.7 - - - +
522B THR* 1.3 63.6 + - - +
527B HIS* 3.5 1.9 - - - -
528B VAL 2.8 36.9 + - - +
530B VAL* 5.3 0.2 - - + -
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Residues in contact with THR 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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499B SER* 4.1 0.9 - - - -
503B GLY* 3.1 3.1 - - - -
504B ASN* 2.8 52.6 + - - +
520B VAL* 3.5 8.8 - - - +
521B ARG* 1.3 78.2 + - - +
523B VAL* 1.3 65.0 + - - +
524B GLN 4.0 9.9 - - - +
526B GLN 3.4 8.3 - - - +
527B HIS* 3.0 42.8 + - + +
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Residues in contact with VAL 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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498B ALA* 3.9 14.1 - - + -
499B SER* 3.5 31.9 - - - +
502B ARG* 3.8 21.3 - - + +
503B GLY* 3.7 7.9 - - - -
522B THR* 1.3 78.6 - - - +
524B GLN* 1.3 88.4 + - + +
526B GLN* 3.0 18.0 + - + +
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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