Contacts of the helix formed by residues 508 - 522 (chain A) in PDB entry 4JWE
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 ASN 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A GLY 4.0 1.0 + - - -
507A LEU* 1.4 74.1 - - - +
509A GLU* 1.3 59.8 + - - +
510A ASP* 3.4 10.3 + - - +
511A GLU* 3.0 47.7 + - - +
512A ILE* 2.8 29.9 + - - +
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Residues in contact with GLU 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508A ASN* 1.3 74.0 - - - +
510A ASP* 1.4 58.8 - - - +
512A ILE* 3.3 14.6 + - + +
513A GLN* 3.0 38.4 + - - +
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Residues in contact with ASP 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508A ASN* 3.4 9.2 + - - +
509A GLU* 1.4 76.8 - - - +
511A GLU* 1.3 58.9 + - + +
513A GLN* 3.3 17.3 + - - +
514A LYS* 2.9 41.6 + - - +
517A ARG* 5.0 0.2 + - - -
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Residues in contact with GLU 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A GLY 4.6 1.6 - - - +
507A LEU* 3.4 36.6 - - + +
508A ASN* 3.0 44.9 + - - +
510A ASP* 1.3 73.9 - - + +
512A ILE* 1.3 59.9 + - - +
514A LYS* 3.8 10.3 - - + +
515A MET* 2.9 30.8 + - - +
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Residues in contact with ILE 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A PRO* 3.6 37.0 - - + +
397A LEU* 3.8 36.7 - - + +
442A GLN* 5.4 0.2 - - - +
507A LEU* 3.3 24.0 - - + +
508A ASN 2.8 20.5 + - - +
509A GLU* 3.5 13.7 - - + +
511A GLU* 1.3 73.4 - - - +
513A GLN* 1.4 68.2 + - + +
515A MET* 3.3 3.5 + - - +
516A VAL* 3.1 29.7 + - + +
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Residues in contact with GLN 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A GLU* 3.0 23.2 + - - +
510A ASP* 3.6 20.5 - - - +
512A ILE* 1.4 78.5 - - + +
514A LYS* 1.3 59.7 + - - +
516A VAL* 3.4 7.6 + - - +
517A ARG* 3.0 56.4 + - - +
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Residues in contact with LYS 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510A ASP* 2.9 28.7 + - - +
511A GLU* 3.8 10.5 - - + +
512A ILE 3.4 0.2 - - - -
513A GLN* 1.3 74.4 - - - +
515A MET* 1.4 52.7 + - - +
517A ARG* 3.4 19.4 + - - +
518A ASP* 2.8 42.7 + - - +
456B GLN* 3.9 45.6 + - + +
457B PHE* 4.9 4.6 - - - +
458B ASN* 4.1 23.9 - - - +
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Residues in contact with MET 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A LEU* 3.8 21.1 - - + -
442A GLN 4.3 0.2 - - - +
443A GLY* 3.9 7.6 - - - -
444A GLU* 3.4 27.1 - - + +
445A ARG* 3.7 17.7 - - + -
450A ASP 3.7 23.1 - - - +
451A ASN* 3.9 13.9 - - - +
452A LYS 4.6 1.1 - - - +
507A LEU* 4.0 20.9 - - + -
511A GLU 2.9 18.5 + - - +
512A ILE 3.5 6.1 - - - +
514A LYS* 1.4 75.5 - - - +
516A VAL* 1.4 57.0 + - - +
518A ASP* 3.4 5.6 + - - +
519A ALA* 2.9 31.5 + - - +
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Residues in contact with VAL 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A PRO 5.3 1.3 - - - +
397A LEU* 4.1 17.7 - - + -
414A LYS* 4.1 28.5 - - + +
444A GLU* 4.6 7.0 - - + -
512A ILE* 3.1 21.7 + - + +
513A GLN* 3.4 6.9 + - - +
515A MET* 1.4 73.1 - - - +
517A ARG* 1.4 63.4 + - + +
519A ALA* 3.5 5.9 + - - +
520A GLU* 3.1 37.7 + - - +
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Residues in contact with ARG 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510A ASP 5.0 0.2 + - - -
513A GLN* 3.0 60.5 + - - +
514A LYS* 3.7 21.9 - - - +
516A VAL* 1.4 76.2 - - + +
518A ASP* 1.3 60.1 + - - +
520A GLU* 3.3 16.9 - - - +
521A ALA* 2.9 30.6 + - - +
14C ARG* 4.5 21.4 - - + +
15C PRO 4.4 19.5 - - - +
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Residues in contact with ASP 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A ARG* 4.1 18.1 + - - +
514A LYS* 2.8 27.6 + - - +
515A MET* 3.8 6.0 + - - +
517A ARG* 1.3 69.3 - - - +
519A ALA* 1.4 59.7 + - - +
521A ALA* 3.5 0.8 + - - -
522A ASN* 2.9 36.2 + - - +
456B GLN* 3.4 27.4 + - - +
14C ARG* 3.1 38.1 + - - +
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Residues in contact with ALA 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A GLU* 3.6 31.6 - - + +
445A ARG* 3.8 18.3 - - - +
515A MET 2.9 18.1 + - - +
516A VAL* 3.7 5.4 - - - +
518A ASP* 1.4 73.5 - - - +
520A GLU* 1.3 58.2 + - - +
522A ASN 3.4 2.9 + - - -
523A ALA* 3.0 29.3 + - - +
526A ASP* 4.8 3.5 - - - +
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Residues in contact with GLU 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A VAL* 3.1 31.4 + - - +
517A ARG* 3.3 17.7 - - - +
519A ALA* 1.3 75.2 - - - +
521A ALA* 1.4 61.2 + - - +
522A ASN 3.4 0.7 + - - -
523A ALA* 3.4 19.4 + - - +
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Residues in contact with ALA 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A ARG 2.9 16.1 + - - +
518A ASP 4.1 0.9 - - - +
519A ALA 3.4 0.2 - - - -
520A GLU* 1.4 75.7 - - - +
522A ASN* 1.3 60.5 + - - +
523A ALA 3.5 0.6 + - - -
524A GLU 5.4 0.2 + - - -
14C ARG* 3.5 40.1 + - + +
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Residues in contact with ASN 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ARG* 3.3 33.4 + - - +
518A ASP 2.9 24.8 + - - +
519A ALA 3.4 3.6 - - - +
521A ALA* 1.3 77.7 - - - +
523A ALA* 1.4 52.0 + - - +
524A GLU 3.4 2.0 - - - -
525A ALA* 3.3 17.3 + - + +
526A ASP* 2.8 34.5 + - - +
14C ARG* 3.2 38.1 + - - +
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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