Contacts of the helix formed by residues 504 - 518 (chain B) in PDB entry 4MS0
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 504 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503B PHE* 1.3 70.2 - - - +
505B LEU* 1.3 67.3 + - - +
506B GLU* 3.4 1.8 - - + +
507B LYS* 3.2 26.8 + - + +
508B LEU* 3.0 20.3 + - - +
610B ILE* 5.3 3.0 + - - +
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Residues in contact with LEU 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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460B MET* 3.5 45.5 - - + +
491B VAL* 4.6 5.6 - - + -
495B HIS* 3.8 32.8 - - + +
500B THR 5.9 1.8 - - - +
503B PHE 3.2 6.5 + - - -
504B GLU* 1.3 70.6 - - - +
506B GLU* 1.3 65.3 + - - +
508B LEU* 3.2 8.1 + - + +
509B CYS* 2.9 36.4 + - - -
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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
----------------------------------------------------------
456B TRP* 4.2 16.7 - - + -
460B MET* 4.4 16.2 - - + +
504B GLU* 3.4 1.9 - - + +
505B LEU* 1.3 78.2 - - - +
507B LYS* 1.3 58.2 + - + +
509B CYS* 3.4 2.1 + - - +
510B ARG* 2.9 55.1 + - - +
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Residues in contact with LYS 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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504B GLU* 3.2 24.4 + - + +
506B GLU* 1.3 76.2 - - + +
508B LEU* 1.3 52.8 + - - +
510B ARG* 3.3 9.3 + - - +
511B PHE* 2.7 35.2 + - - +
607B GLY* 3.7 29.9 - - - +
608B HIS* 4.8 0.9 - - - -
609B ASN 3.6 25.6 - - - +
610B ILE* 3.7 16.6 - - + +
612B SER* 4.8 7.2 - - - +
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Residues in contact with LEU 508 (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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490B PHE* 4.5 10.8 - - + -
491B VAL* 4.6 11.0 - - + -
494B VAL* 4.4 13.0 - - + -
495B HIS* 4.2 21.5 - - + +
503B PHE* 3.9 43.7 - - + +
504B GLU 3.0 17.2 + - - +
505B LEU* 3.6 7.0 - - + +
507B LYS* 1.3 72.1 - - - +
509B CYS* 1.3 57.2 + - - +
511B PHE* 3.3 2.7 + - + +
512B ILE* 2.8 62.4 + - + +
558B ILE* 4.7 7.4 - - + -
610B ILE* 3.7 11.2 - - + +
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Residues in contact with CYS 509 (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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456B TRP* 3.6 20.5 - - + +
459B LEU* 3.7 30.9 - - + +
460B MET* 3.6 26.9 - - + -
491B VAL* 4.4 8.5 - - - -
505B LEU* 2.9 34.0 + - - +
506B GLU 3.9 3.4 - - - +
508B LEU* 1.3 74.5 - - - +
510B ARG* 1.3 64.4 + - - +
512B ILE* 4.6 0.7 - - - -
513B MET* 3.1 31.7 + - - +
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Residues in contact with ARG 510 (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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451B CYS* 3.4 12.1 - - - +
456B TRP* 3.6 61.2 - - + +
506B GLU* 2.9 31.6 + - - +
507B LYS* 3.4 21.3 - - - +
509B CYS* 1.3 75.3 - - - +
511B PHE* 1.3 64.0 + - - +
513B MET 3.3 1.0 + - - -
514B SER* 3.0 27.5 + - - -
606B GLU 4.7 1.3 - - - -
607B GLY* 2.9 40.2 + - - +
608B HIS* 3.9 20.0 - - + +
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Residues in contact with PHE 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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507B LYS 2.7 21.2 + - - +
508B LEU* 3.3 6.9 + - + +
510B ARG* 1.3 74.1 - - - +
512B ILE* 1.3 72.1 + - + +
514B SER* 3.2 2.3 + - - -
515B VAL* 2.9 40.2 + - + +
558B ILE* 3.7 37.7 - - + -
561B LEU* 4.8 3.8 - - + -
562B CYS* 3.7 25.4 - - - -
599B THR* 5.0 2.7 - - + -
602B ILE* 4.0 22.4 - - + -
603B LEU* 3.6 30.1 - - + -
608B HIS* 3.7 27.1 - + - +
610B ILE* 3.8 15.0 - - + -
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Residues in contact with ILE 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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459B LEU* 3.9 5.6 - - + -
487B PRO* 3.9 30.3 - - + +
490B PHE* 3.4 33.9 - - + -
491B VAL* 3.4 33.0 - - + +
508B LEU* 2.8 36.5 + - + +
509B CYS 4.0 3.8 - - - +
511B PHE* 1.3 78.6 - - + +
513B MET* 1.3 59.9 + - - +
515B VAL* 3.3 6.4 + - - +
516B LYS* 3.1 24.9 + - - +
527B TRP* 4.1 15.7 - - + -
561B LEU* 4.2 5.6 - - + -
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Residues in contact with MET 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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451B CYS* 3.4 25.1 - - + +
455B GLU* 3.8 45.9 - - + +
456B TRP* 4.1 2.2 - - - -
459B LEU* 3.9 15.0 - - + -
487B PRO* 3.9 32.8 - - + -
509B CYS 3.1 19.3 + - - +
512B ILE* 1.3 75.1 - - - +
514B SER* 1.3 64.0 + - - +
516B LYS* 3.6 26.2 + - + +
517B LYS* 3.3 22.0 + - - +
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Residues in contact with SER 514 (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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449B SER 3.8 15.5 - - - -
450B ILE* 3.6 1.8 - - - -
451B CYS* 3.1 22.4 + - - +
510B ARG 3.0 9.5 + - - -
511B PHE 3.7 3.1 - - - -
513B MET* 1.3 73.5 - - - +
515B VAL* 1.3 61.4 + - - +
517B LYS* 3.1 10.9 + - - +
518B ASN* 2.7 26.0 + - - -
602B ILE* 4.2 8.1 - - - -
605B LEU* 4.7 0.7 - - - -
608B HIS* 2.5 38.3 + - - -
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Residues in contact with VAL 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B PHE* 2.9 46.0 + - + +
512B ILE 3.3 8.9 + - - +
514B SER* 1.3 76.1 - - - +
516B LYS* 1.3 62.6 + - - +
518B ASN* 3.0 12.6 + - - -
519B TYR* 3.4 34.3 + - + -
527B TRP* 4.1 2.5 - - + -
561B LEU* 3.9 25.6 - - + +
562B CYS* 3.8 13.9 - - - -
565B LEU* 3.6 7.1 - - + +
602B ILE* 4.0 18.8 - - + +
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Residues in contact with LYS 516 (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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455B GLU* 5.9 0.8 + - - -
487B PRO* 5.0 6.3 - - + -
512B ILE 3.1 12.5 + - - +
513B MET* 3.7 33.0 - - + +
515B VAL* 1.3 76.1 - - - +
517B LYS* 1.3 67.5 + - + +
519B TYR* 3.1 22.4 + - - +
527B TRP* 3.7 57.6 - - + +
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Residues in contact with LYS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B SER* 4.7 12.3 - - - -
450B ILE 3.0 31.0 + - - +
451B CYS* 4.3 0.7 - - - -
452B THR* 3.6 17.6 - - - +
455B GLU* 3.0 39.0 + - - +
513B MET 3.3 9.2 + - - +
514B SER* 3.1 12.5 + - - +
516B LYS* 1.3 83.4 - - + +
518B ASN* 1.3 61.3 + - - +
519B TYR 3.3 8.1 + - - +
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Residues in contact with ASN 518 (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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449B SER* 2.8 48.2 + - - +
514B SER 2.7 21.6 + - - -
515B VAL 3.0 10.9 + - - +
517B LYS* 1.3 74.6 - - - +
519B TYR* 1.3 58.9 + - - +
520B ARG* 5.3 1.1 - - - -
565B LEU* 3.7 14.7 - - + +
566B ASP* 3.0 33.1 + - - +
598B GLN* 4.0 14.5 + - - +
602B ILE* 3.4 21.0 - - + +
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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