Contacts of the strand formed by residues 511 - 521 (chain B) in PDB entry 3N9V
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 TRP 511 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461B LYS* 4.0 50.3 + - + +
464B ILE* 4.4 17.7 - - + +
499B GLN* 3.6 29.4 - - - -
500B PRO* 4.0 18.2 - - + -
502B TYR 4.2 9.4 - - - -
503B LYS 3.5 19.3 - - - -
504B TYR* 3.7 23.8 - + - -
505B ASP* 3.1 18.2 - - - +
509B ASP 5.2 3.4 + - - -
510B ASP* 1.3 79.6 - - - +
512B ASP* 1.3 61.6 + - - +
520B PRO* 4.1 27.8 - - + -
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Residues in contact with ASP 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B LYS* 5.2 7.6 + - - -
503B LYS* 3.0 59.1 + - + +
504B TYR 4.7 2.0 - - - +
505B ASP* 3.6 14.6 - - - +
511B TRP* 1.3 76.1 - - - +
519B ALA 4.6 16.1 + - - -
520B PRO* 6.5 0.4 - - - -
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Residues in contact with ALA 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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405B ILE* 6.6 0.2 - - + -
451B ARG* 4.9 15.0 + - + +
452B ILE 5.6 6.3 - - - +
457B VAL* 4.5 24.0 - - + +
461B LYS* 6.1 0.8 - - - +
502B TYR* 4.8 5.2 - - - +
503B LYS* 5.2 4.2 + - - +
512B ASP 4.6 17.1 + - - -
520B PRO* 1.4 78.4 - - - +
521B ALA* 4.4 4.2 - - - +
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Residues in contact with PRO 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B ARG* 5.1 0.7 - - - +
452B ILE* 3.6 22.0 + - - +
457B VAL* 5.0 4.9 - - + +
460B VAL* 4.3 26.5 - - + +
461B LYS* 4.3 31.4 - - + -
500B PRO* 4.5 7.2 - - + -
502B TYR 3.4 15.3 - - - +
503B LYS 4.4 1.3 - - - +
511B TRP* 4.1 28.7 - - + -
512B ASP 6.5 0.4 - - - -
519B ALA* 1.4 88.2 - - - +
521B ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 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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450B TYR 3.8 8.1 - - - +
451B ARG* 3.3 38.4 - - - -
452B ILE* 4.5 8.1 - - - -
500B PRO* 3.4 10.4 - - - +
501B THR 3.2 20.1 + - - -
502B TYR* 3.0 15.3 + - + +
519B ALA 4.4 1.6 - - - +
520B PRO* 1.3 78.1 - - - +
522B TRP* 1.3 60.0 + - - +
523B CYS* 3.3 13.2 + - - -
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Residues in contact with TRP 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B TYR 3.5 9.4 + - - +
452B ILE* 4.4 5.1 - - + +
469B PHE* 3.8 40.4 - + + -
472B LEU* 4.1 20.4 - - + -
473B TYR* 3.9 24.5 - - + -
476B ASP* 4.0 18.5 + - + -
496B LEU* 3.7 35.7 - - + +
498B PHE* 2.8 50.7 + + - -
500B PRO* 3.4 28.9 - - + -
501B THR* 4.4 4.0 - - + -
521B ALA* 1.3 68.5 - - - +
523B CYS* 1.3 61.5 + - - +
524B ASP 3.2 3.8 - - - +
525B ARG* 2.5 47.5 + - - +
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Residues in contact with CYS 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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447B ASP* 3.4 15.5 - - - +
448B LEU 3.0 25.8 + - - -
449B ASN* 3.2 28.1 + - - +
450B TYR 4.1 2.2 + - - -
451B ARG* 3.6 15.3 - - - -
501B THR* 4.0 1.4 + - - -
502B TYR* 3.5 34.3 - - + -
521B ALA* 3.3 14.1 + - - -
522B TRP* 1.3 76.8 - - - +
524B ASP* 1.3 70.2 + - - +
525B ARG* 3.7 5.5 - - - +
549B HIS* 3.9 5.6 - - + -
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Residues in contact with ASP 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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271B THR* 4.5 11.1 + - + +
273B ASN* 4.3 7.8 + - - +
302B GLN* 4.4 2.3 - - - +
446B GLY 3.4 6.1 - - - +
447B ASP* 3.6 22.7 + - - +
498B PHE* 4.6 6.1 - - - -
501B THR* 2.7 29.4 + - - +
522B TRP* 3.2 1.8 - - - +
523B CYS* 1.3 78.2 - - - +
525B ARG* 1.3 65.7 + - - +
538B TYR* 4.4 1.9 + - - -
549B HIS* 2.8 33.7 + - - +
550B LYS 4.4 5.8 - - - +
552B VAL* 3.7 31.3 - - + +
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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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271B THR* 4.2 2.1 - - - +
444B TRP 4.0 0.3 - - - +
445B LEU* 3.3 2.9 - - - -
446B GLY 3.0 31.8 + - - -
448B LEU* 4.0 11.6 - - + +
450B TYR* 4.6 4.6 + - + +
473B TYR* 4.6 1.0 - - - -
476B ASP* 2.4 44.4 + - - -
478B LEU* 3.3 32.1 - - + +
493B GLU* 3.0 40.0 + - - +
496B LEU* 3.8 10.5 - - - +
522B TRP* 2.5 39.2 + - - +
523B CYS 3.7 9.9 - - - +
524B ASP* 1.3 83.7 - - - +
526B ILE* 1.3 65.6 + - - +
527B LEU* 4.0 16.0 - - + +
538B TYR* 3.7 5.4 - - - -
552B VAL* 5.3 0.2 - - - -
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Residues in contact with ILE 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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269B ALA* 3.5 45.3 - - + +
270B GLY* 4.5 0.9 - - - +
271B THR* 4.3 7.2 - - + -
443B LEU* 5.5 3.1 - - + -
444B TRP 3.3 10.1 - - - +
445B LEU* 4.1 11.7 - - + -
493B GLU* 3.7 9.7 - - - +
525B ARG* 1.3 78.7 - - - +
527B LEU* 1.3 74.2 + - - +
528B TRP* 4.5 4.4 - - - -
535B GLN* 4.9 0.2 + - - -
538B TYR* 3.3 25.8 + - + -
552B VAL* 4.1 9.6 - - + +
553B SER* 3.8 8.5 - - - -
554B SER* 3.6 21.5 - - - +
556B PHE* 4.2 17.9 - - + -
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Residues in contact with LEU 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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443B LEU* 3.8 2.1 - - - +
444B TRP* 2.8 33.3 + - + +
448B LEU* 3.9 28.3 - - + -
478B LEU* 4.3 12.3 - - + -
482B VAL* 5.0 8.1 - - + -
488B PHE* 4.2 27.8 - - + -
491B PHE* 4.3 21.5 - - + -
492B THR 3.3 8.7 - - - +
493B GLU* 3.8 27.1 - - + +
525B ARG* 4.0 11.4 - - + -
526B ILE* 1.3 85.5 - - - +
528B TRP* 1.3 67.7 + - - +
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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