Contacts of the helix formed by residues 520 - 542 (chain B) in PDB entry 4JGV
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 GLU 520 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B GLU 5.3 0.2 - - - +
430B LEU* 5.0 2.8 - - + +
431B SER* 4.1 21.2 + - - -
434B ASP* 2.9 15.3 + - - +
518B LEU* 4.7 0.2 - - - -
519B GLN* 1.3 92.1 - - + +
521B PRO* 1.3 65.6 - - - +
522B ARG 2.9 5.4 + - - -
523B ARG* 3.0 45.0 + - + +
524B VAL* 3.4 11.8 + - + +
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Residues in contact with PRO 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B ASP* 4.0 15.9 - - - +
518B LEU* 3.4 35.0 - - + +
519B GLN 3.2 9.9 - - - +
520B GLU* 1.3 89.5 - - - +
522B ARG* 1.3 61.7 + - + +
524B VAL* 3.5 4.5 + - - +
525B GLU* 3.0 37.8 + - - +
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Residues in contact with ARG 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B GLU 2.9 1.6 + - - -
521B PRO* 1.3 80.1 - - + +
523B ARG* 1.3 58.7 + - + +
525B GLU* 3.3 21.2 + - - +
526B GLU* 2.8 55.4 + - - +
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Residues in contact with ARG 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B GLY* 5.1 3.0 + - - -
429B GLU* 2.7 44.3 + - - +
430B LEU* 3.9 21.4 - - + +
520B GLU* 3.0 41.3 + - + +
522B ARG* 1.3 75.1 - - + +
524B VAL* 1.3 61.1 + - - +
526B GLU* 3.4 14.6 + - - +
527B LEU* 2.9 29.8 + - - +
530B ARG* 4.3 18.6 + - - +
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Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LEU* 4.2 17.7 - - + -
434B ASP* 4.6 4.5 - - - +
438B LEU* 4.2 19.3 - - + -
512B ILE* 3.6 7.9 - - + +
513B THR* 3.7 40.8 - - - +
514B ASP* 4.6 0.7 - - - +
518B LEU* 3.9 22.4 - - + -
520B GLU 3.4 10.9 + - - +
521B PRO 3.5 9.2 - - - +
522B ARG 3.2 0.2 - - - -
523B ARG* 1.3 76.9 - - - +
525B GLU* 1.3 59.0 + - + +
527B LEU* 3.2 7.0 + - - +
528B GLN* 2.8 27.9 + - - +
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Residues in contact with GLU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B ASP* 3.0 34.9 - - - +
521B PRO* 3.0 26.1 + - - +
522B ARG* 3.3 25.0 + - - +
524B VAL* 1.3 76.7 - - + +
526B GLU* 1.3 57.7 + - + +
528B GLN* 3.2 13.8 - - - +
529B ASN* 2.9 36.5 + - - +
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Residues in contact with GLU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B ARG* 2.8 41.1 + - - +
523B ARG* 3.7 17.5 + - - +
525B GLU* 1.3 75.0 - - + +
527B LEU* 1.3 57.8 - - - +
529B ASN* 3.0 16.6 + - + +
530B ARG* 2.9 46.1 + - - +
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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
----------------------------------------------------------
364B LEU* 6.1 2.7 - - + -
425B PRO 3.4 19.3 - - - +
426B GLY* 3.8 27.6 - - - +
427B PHE* 3.9 5.8 - - - +
430B LEU* 4.5 12.6 - - + -
512B ILE* 3.9 27.1 - - + -
523B ARG 2.9 17.5 + - - +
524B VAL* 3.5 5.6 - - - +
526B GLU* 1.3 74.5 - - - +
528B GLN* 1.3 65.3 + - - +
530B ARG* 3.3 33.4 + - + +
531B ILE* 3.1 41.0 + - + +
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Residues in contact with GLN 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B LEU* 3.6 33.6 + - + +
512B ILE* 2.7 36.8 + - - +
513B THR* 3.8 18.3 + - - -
514B ASP 5.3 1.1 - - - -
524B VAL 2.8 12.1 + - - +
525B GLU* 3.2 17.4 - - - +
527B LEU* 1.3 74.9 - - - +
529B ASN* 1.3 61.1 + - - +
531B ILE* 3.1 4.5 + - - +
532B ALA* 2.8 30.2 + - - +
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Residues in contact with ASN 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B GLU* 2.9 23.9 + - - +
526B GLU* 3.0 18.7 + - - +
528B GLN* 1.3 78.5 - - - +
530B ARG* 1.3 64.3 + - - +
532B ALA* 3.2 8.3 + - - +
533B SER* 2.9 28.3 + - - +
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Residues in contact with ARG 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU* 3.9 14.4 - - + +
425B PRO 5.1 2.2 + - - -
426B GLY* 5.2 5.5 - - - -
523B ARG* 4.3 18.2 + - - +
526B GLU* 2.9 26.8 + - - +
527B LEU* 3.5 51.7 - - + +
529B ASN* 1.3 76.9 - - - +
531B ILE* 1.3 58.0 + - - +
533B SER* 3.3 7.8 + - - -
534B CYS* 3.1 25.6 + - - +
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Residues in contact with ILE 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU* 4.2 13.2 - - + -
368B LEU* 4.2 20.4 - - + -
424B ILE* 4.5 7.4 - - + -
505B CYS* 3.8 25.3 - - - +
508B ALA* 4.1 13.9 - - + +
509B LEU* 3.9 12.1 - - + -
512B ILE* 3.9 32.1 - - + -
527B LEU* 3.1 30.3 + - + +
528B GLN* 3.7 3.8 - - - +
530B ARG* 1.3 72.6 - - - +
532B ALA* 1.3 62.1 + - - +
534B CYS* 3.3 7.7 - - - +
535B LEU* 3.0 25.1 + - - +
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Residues in contact with ALA 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B LEU* 4.4 15.4 - - + +
528B GLN* 2.8 17.2 + - - +
529B ASN* 3.6 8.7 - - - +
531B ILE* 1.3 74.6 - - - +
533B SER* 1.3 63.8 + - - +
535B LEU* 3.3 8.6 + - - +
536B LYS* 2.9 25.0 + - - +
556B LEU* 6.4 1.6 - - + -
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Residues in contact with SER 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ASN* 2.9 16.9 + - - +
530B ARG* 3.4 10.0 + - - -
532B ALA* 1.3 72.9 - - - +
534B CYS* 1.3 67.5 + - - +
536B LYS* 3.2 7.0 + - - +
537B GLU* 2.9 44.1 + - - -
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Residues in contact with CYS 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ALA* 4.4 7.6 - - + -
364B LEU* 3.8 20.0 - - + -
365B LEU* 3.5 52.4 - - - +
368B LEU* 4.3 1.1 - - + -
505B CYS* 4.1 5.2 - - - -
530B ARG 3.1 10.1 + - - +
531B ILE* 3.3 11.2 - - - +
533B SER* 1.3 80.7 - - - +
535B LEU* 1.3 57.1 + - - +
537B GLU* 3.9 8.6 - - - +
538B HIS* 3.0 28.8 + - - +
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Residues in contact with LEU 535 (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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502B ALA* 3.6 39.3 - - + +
505B CYS* 3.8 20.0 - - + -
506B LEU* 4.8 2.5 - - + +
509B LEU* 4.1 21.8 - - + -
531B ILE 3.0 14.1 + - - +
532B ALA* 3.6 9.0 - - - +
533B SER 3.2 0.2 - - - -
534B CYS* 1.3 73.6 - - - +
536B LYS* 1.3 61.6 + - - +
538B HIS* 3.1 7.1 + - + +
539B VAL* 2.9 43.9 + - + +
552B LEU 6.1 0.4 - - - +
555B LEU* 3.8 22.4 - - + -
556B LEU* 4.3 12.8 - - + -
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Residues in contact with LYS 536 (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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532B ALA 2.9 16.3 + - - +
533B SER* 3.6 6.7 - - - +
535B LEU* 1.3 77.7 - - - +
537B GLU* 1.3 65.1 + - + +
539B VAL* 3.1 11.7 - - - +
540B ALA* 3.0 24.7 + - + +
552B LEU* 3.4 37.0 - - + -
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Residues in contact with GLU 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B SER* 2.9 36.2 + - - +
534B CYS* 3.9 6.8 - - - +
536B LYS* 1.3 78.4 - - + +
538B HIS* 1.3 57.7 - - - +
540B ALA* 3.3 6.5 + - - +
541B ALA* 2.8 30.7 + - - +
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Residues in contact with HIS 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 3.8 28.4 - - + +
499B ASP* 2.8 38.8 + - - -
501B PRO* 3.5 23.1 - - + +
502B ALA* 4.0 16.8 - - + -
505B CYS* 5.7 0.2 - - - -
534B CYS 3.0 15.7 + - - +
535B LEU* 3.4 9.9 - - + +
537B GLU* 1.3 76.6 - - - +
539B VAL* 1.3 69.2 + - + +
541B ALA* 3.5 8.8 - - - +
542B VAL* 3.2 35.8 + - + +
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Residues in contact with VAL 539 (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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502B ALA* 5.0 3.4 - - + -
535B LEU* 2.9 39.2 + - + +
536B LYS* 3.1 24.4 + - + +
538B HIS* 1.3 81.6 - - + +
540B ALA* 1.3 62.8 + - + +
542B VAL* 3.3 21.2 + - - +
551B CYS* 5.9 6.3 - - + -
552B LEU* 4.7 28.0 - - + +
555B LEU* 4.8 16.8 - - + -
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Residues in contact with ALA 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LYS* 3.0 16.5 + - + +
537B GLU* 3.6 6.7 - - - +
539B VAL* 1.3 78.7 - - + +
541B ALA* 1.3 66.4 + - - +
542B VAL 3.3 6.9 + - - +
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Residues in contact with ALA 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B GLU 2.8 21.2 + - - +
538B HIS* 3.5 13.2 - - - +
540B ALA* 1.3 73.7 - - - +
542B VAL* 1.3 62.4 + - + +
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Residues in contact with VAL 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ASP* 4.0 9.4 - - - +
538B HIS* 3.2 36.1 + - + +
539B VAL* 3.3 19.7 - - - +
540B ALA 3.2 5.7 - - - +
541B ALA* 1.3 82.5 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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