Contacts of the helix formed by residues 500 - 515 (chain B) in PDB entry 2N4Q
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 ASP 500 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499B MET* 1.3 80.9 - - - +
501B LYS* 1.3 81.1 + - - +
502B ALA* 2.9 16.9 + - - +
503B TYR* 3.5 15.6 + - - +
504B LEU* 4.6 7.7 + - - +
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Residues in contact with LYS 501 (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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329A GLY 4.7 14.0 + - - -
499B MET* 5.1 14.1 - - + +
500B ASP* 1.3 91.3 + - - +
502B ALA* 1.3 54.3 + - - +
503B TYR 3.2 0.4 - - - -
504B LEU* 2.9 25.5 + - + +
505B ASP* 2.6 42.2 + - + +
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Residues in contact with ALA 502 (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 MET* 5.6 5.1 - - + +
500B ASP* 2.9 8.1 - - - +
501B LYS* 1.3 75.9 - - - +
503B TYR* 1.3 64.8 + - - +
505B ASP* 3.0 19.1 + - - +
506B GLU* 3.0 20.1 + - + +
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Residues in contact with TYR 503 (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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500B ASP 3.5 9.7 + - - +
501B LYS 3.2 0.4 - - - -
502B ALA* 1.3 81.5 - - - +
504B LEU* 1.3 66.7 + - + +
506B GLU* 3.0 16.3 + - + +
507B LEU* 3.1 32.1 + - + +
550B LEU 5.6 1.5 + - - -
551B ASP 4.5 0.5 - - - -
552B LYS* 3.5 40.6 + - + +
555B VAL* 4.3 19.4 - - + +
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Residues in contact with LEU 504 (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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331A PRO 5.4 7.4 - - - +
333A LEU* 5.8 6.7 - - + +
500B ASP* 5.2 7.4 - - - +
501B LYS* 2.9 31.8 + - + +
503B TYR* 1.3 78.2 - - + +
505B ASP* 1.3 63.3 + - - +
507B LEU* 3.3 12.4 + - + +
508B VAL* 3.0 35.7 + - + +
548B CYS* 3.7 37.0 - - + -
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Residues in contact with ASP 505 (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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501B LYS* 2.6 21.4 + - - +
502B ALA* 3.0 18.6 - - - +
504B LEU* 1.3 73.5 - - - +
506B GLU* 1.3 56.3 + - + +
508B VAL* 3.3 5.9 + - - +
509B GLU* 2.9 46.7 + - - +
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Residues in contact with GLU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B ALA* 3.0 16.0 + - + +
503B TYR* 3.5 9.4 - - + +
505B ASP* 1.3 74.1 - - + +
507B LEU* 1.3 56.5 + - - +
509B GLU* 3.0 7.7 + - - +
510B LEU* 2.6 38.9 + - + +
555B VAL* 5.8 7.0 - - + -
559B GLN* 3.9 18.8 - - - +
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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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333A LEU* 4.2 5.3 - - + +
503B TYR* 3.1 30.5 + - + +
504B LEU* 3.5 16.4 - - + +
506B GLU* 1.3 77.8 - - - +
508B VAL* 1.3 58.7 + - + +
510B LEU* 3.6 9.1 - - + +
511B HIS* 3.0 31.9 + - - +
547B LEU* 3.4 55.4 - - + +
548B CYS* 3.7 20.2 - - + +
550B LEU 6.0 0.4 - - - +
555B VAL* 4.0 27.1 - - + -
558B LEU* 5.7 0.4 - - + -
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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
----------------------------------------------------------
333A LEU* 3.8 34.8 - - + -
504B LEU* 3.0 23.2 + - + +
505B ASP* 3.6 8.3 - - - +
507B LEU* 1.3 77.1 - - + +
509B GLU* 1.3 59.4 + - + +
511B HIS* 3.9 1.0 - - - +
512B ARG* 2.8 56.2 + - + +
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Residues in contact with GLU 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ASP* 2.9 36.0 + - - +
506B GLU* 3.5 7.4 - - - +
508B VAL* 1.3 76.6 - - + +
510B LEU* 1.3 63.7 + - - +
512B ARG* 3.4 23.5 + - - +
513B ARG* 3.0 33.5 + - - +
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Residues in contact with LEU 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B GLU 2.6 21.9 + - - +
507B LEU* 3.6 9.4 - - + +
509B GLU* 1.3 69.1 - - - +
511B HIS* 1.3 81.8 + - - +
513B ARG* 3.0 11.5 + - - +
514B LEU* 3.0 26.2 + - + +
547B LEU* 5.0 3.6 - - + -
555B VAL* 4.4 7.4 - - + +
558B LEU* 3.8 40.8 - - + -
559B GLN* 3.6 31.6 - - + -
562B LEU* 3.8 22.9 - - + +
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Residues in contact with HIS 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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333A LEU* 4.1 15.5 - - + -
334A ILE 5.6 0.9 - - - -
335A ALA* 3.0 34.2 - - + +
337A ILE* 6.0 0.4 - - - +
507B LEU 3.0 13.8 + - - +
508B VAL 4.0 2.5 - - - +
510B LEU* 1.3 88.8 - - + +
512B ARG* 1.3 51.9 + - + +
514B LEU* 3.1 21.7 + - + +
515B MET* 2.7 47.2 + - - +
526B ILE* 6.3 2.2 - - + -
545B PHE* 4.1 11.7 - + - -
547B LEU* 3.4 38.8 - - + +
558B LEU* 5.9 1.8 - - + -
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Residues in contact with ARG 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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508B VAL* 2.8 42.8 + - + +
509B GLU* 3.4 21.9 + - - +
511B HIS* 1.3 77.7 - - + +
513B ARG* 1.3 62.6 + - + +
515B MET* 3.2 14.9 + - - +
516B THR* 3.1 18.3 - - - +
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Residues in contact with ARG 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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509B GLU* 3.0 21.2 + - - +
510B LEU* 3.5 10.1 - - - +
512B ARG* 1.3 75.6 - - + +
514B LEU* 1.3 60.1 + - - +
516B THR* 2.5 32.3 + - - -
517B LEU* 3.5 10.9 + - - +
562B LEU* 4.8 21.6 - - + +
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Residues in contact with LEU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B LEU* 3.0 16.9 + - + +
511B HIS* 3.4 30.1 - - + +
513B ARG* 1.3 71.6 - - - +
515B MET* 1.3 60.9 + - - +
516B THR 2.7 15.8 + - - -
517B LEU* 2.7 31.6 + - + +
522B ILE* 5.3 0.7 - - + -
523B LEU* 4.2 22.3 - - + +
526B ILE* 3.4 33.7 - - + -
558B LEU* 5.8 1.8 - - + -
562B LEU* 4.5 23.0 - - + +
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Residues in contact with MET 515 (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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335A ALA* 6.1 2.7 - - + -
511B HIS* 2.7 28.4 + - - +
512B ARG* 3.2 15.2 + - - +
514B LEU* 1.3 77.9 - - - +
516B THR* 1.3 58.8 + - + +
517B LEU 3.6 3.2 - - - +
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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