Contacts of the helix formed by residues 499 - 515 (chain A) in PDB entry 5C16
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 PRO 499 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A MET* 3.8 17.7 - - + +
381A ARG* 3.7 18.8 - - + +
384A LEU* 3.6 34.3 - - + -
409A TRP* 4.3 6.5 - - + -
498A SER* 1.3 88.3 - - - +
500A ILE* 1.3 53.9 + - - +
501A PHE 3.3 2.9 - - - +
502A LEU* 3.2 18.8 + - + +
503A GLN* 2.7 37.7 + - - +
534A TYR* 5.3 4.0 - - - +
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Residues in contact with ILE 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ILE* 3.9 22.2 - - + -
380A MET* 4.3 14.4 - - + -
443A ASP* 3.6 39.0 - - + +
444A ARG* 5.7 4.7 - - + -
447A GLN* 3.0 35.7 + - - +
474A TRP* 3.9 4.9 - - + -
479A HIS* 3.6 22.4 - - + -
484A ARG* 4.4 0.9 - - - -
498A SER* 3.0 30.1 + - - +
499A PRO* 1.3 75.4 - - - +
501A PHE* 1.3 63.3 + - - +
503A GLN* 4.3 7.0 - - - +
504A PHE* 3.0 11.1 + - - +
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Residues in contact with PHE 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A PHE* 5.9 0.2 - + - -
470A VAL* 3.9 27.4 - - + -
474A TRP* 3.5 47.6 - + + -
479A HIS* 4.2 5.1 + - - +
481A PHE* 3.6 27.8 - + + -
498A SER 4.8 0.6 + - - -
499A PRO* 3.3 0.6 - - - +
500A ILE* 1.3 75.9 - - - +
502A LEU* 1.3 67.8 - - - +
504A PHE* 3.1 22.2 + + - +
505A VAL* 2.9 42.1 + - + +
529A ILE* 3.9 21.3 - - + -
530A LEU* 4.6 2.0 - - + -
533A LEU* 4.0 19.7 - - + -
541A PHE* 3.9 11.0 - + - -
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Residues in contact with LEU 502 (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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177A LYS 5.5 0.7 - - - +
179A MET* 6.0 0.4 - - - -
384A LEU* 4.3 13.0 - - + -
409A TRP* 3.8 16.2 - - + -
499A PRO* 3.2 18.0 + - + +
501A PHE* 1.3 78.2 - - - +
503A GLN* 1.3 59.0 + - - +
505A VAL* 2.9 19.6 + - - +
506A ASP* 2.9 13.9 + - - +
530A LEU* 4.0 27.2 - - + +
533A LEU* 4.9 5.8 - - + +
534A TYR* 3.7 24.0 - - + +
597A TRP* 6.0 0.4 - - + -
600A TYR* 3.8 28.3 - - + +
601A TYR* 3.6 30.7 - - + +
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Residues in contact with GLN 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE* 5.9 0.7 - - - +
380A MET* 3.1 46.6 - - - +
409A TRP* 4.0 27.6 - - + -
412A TYR* 3.7 16.7 - - - +
413A ILE* 3.8 13.8 - - + +
416A LEU* 3.5 21.0 - - + +
447A GLN* 2.9 22.2 + - - +
499A PRO 2.7 20.2 + - - +
500A ILE* 3.7 6.5 - - - +
502A LEU* 1.3 72.9 - - - +
504A PHE* 1.3 62.5 + - - +
506A ASP* 3.4 4.9 + - - +
507A CYS* 3.1 22.7 + - - -
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Residues in contact with PHE 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A GLN* 4.1 12.3 - - + +
450A SER* 3.2 32.1 - - - -
451A LEU* 3.8 25.1 - - + -
454A LEU* 5.7 0.7 - - + -
466A PHE* 4.0 24.2 - + - -
469A LEU* 5.1 4.5 - - + -
470A VAL* 4.6 3.1 - - + -
474A TRP* 3.5 31.6 - + + -
500A ILE 3.0 10.4 + - - +
501A PHE* 3.1 34.7 + + - +
503A GLN* 1.3 78.2 - - - +
505A VAL* 1.3 68.1 + - + +
507A CYS* 3.1 10.8 + - - +
508A VAL* 3.0 41.4 + - + +
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Residues in contact with VAL 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A PHE* 5.7 4.0 - - + -
501A PHE* 2.9 37.3 + - + +
502A LEU 2.9 11.2 + - - +
504A PHE* 1.3 84.3 - - + +
506A ASP* 1.3 57.9 + - - +
508A VAL* 3.2 7.0 + - - +
509A TRP* 2.9 26.9 + - - +
526A LEU* 3.9 35.2 - - + +
529A ILE* 4.9 5.2 - - + -
530A LEU* 3.7 26.5 - - + -
597A TRP* 3.9 12.8 - - + -
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Residues in contact with ASP 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TRP* 3.1 8.3 + - - -
410A LEU* 5.3 0.9 - - - +
413A ILE* 3.6 17.5 - - + +
502A LEU 2.9 9.8 + - - +
503A GLN* 3.5 10.5 - - - +
505A VAL* 1.3 75.6 - - - +
507A CYS* 1.3 65.0 + - - +
509A TRP* 2.9 5.2 + - - +
510A GLN* 2.9 46.3 + - - +
597A TRP* 3.9 21.7 + - + +
601A TYR* 2.5 44.0 + - - +
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Residues in contact with CYS 507 (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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413A ILE* 3.9 33.9 - - - -
416A LEU* 4.1 14.8 - - - -
417A LEU* 4.0 11.0 - - + +
451A LEU* 3.8 30.1 - - + -
503A GLN 3.1 15.8 + - - -
504A PHE* 3.1 9.9 + - - +
506A ASP* 1.3 77.2 + - - +
508A VAL* 1.3 63.4 + - - +
510A GLN* 3.0 27.5 - - - +
511A MET* 3.1 10.7 + - - +
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Residues in contact with VAL 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 4.1 4.0 - - + +
454A LEU* 4.1 14.8 - - + -
466A PHE* 3.7 14.4 - - + -
504A PHE* 3.0 45.5 + - + +
505A VAL* 3.4 9.9 - - - +
507A CYS* 1.3 75.1 - - - +
509A TRP* 1.3 59.4 + - - +
511A MET* 2.9 25.5 + - - +
512A THR* 3.0 11.7 + - + +
519A PHE* 5.3 0.7 - - + -
521A PHE* 3.9 20.0 - - + -
526A LEU* 3.9 27.4 - - + -
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Residues in contact with TRP 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A VAL 2.9 13.3 + - - +
506A ASP 2.9 9.8 + - - +
508A VAL* 1.3 75.9 - - - +
510A GLN* 1.3 81.9 + - - +
512A THR* 2.8 29.5 + - - -
513A ARG* 3.0 33.2 + - + +
523A GLU* 3.2 34.1 + - + +
526A LEU* 3.7 16.6 - - + -
595A GLU* 3.9 23.3 - - + -
596A LEU 4.3 5.6 - - - -
597A TRP* 3.3 67.8 - + + -
598A VAL* 5.1 1.6 - - + -
599A ASN* 5.9 0.9 - - + -
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Residues in contact with GLN 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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410A LEU* 4.5 4.8 - - - +
413A ILE* 3.8 16.8 - - + +
417A LEU* 4.0 14.8 - - + -
506A ASP* 2.9 37.9 + - - +
507A CYS* 3.0 16.8 + - - +
509A TRP* 1.3 89.9 - - - +
511A MET* 1.3 59.2 - - - +
513A ARG* 3.3 11.2 + - - +
514A GLN* 3.0 29.2 + - - +
587A PRO* 6.0 0.9 - - + -
594A LEU* 3.8 17.1 - - + +
595A GLU 3.0 41.0 + - - +
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Residues in contact with MET 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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417A LEU* 4.2 6.3 - - + -
451A LEU* 4.4 12.6 - - - -
454A LEU* 4.1 20.0 - - + +
455A MET* 3.6 46.0 - - + +
507A CYS 3.1 10.5 + - - +
508A VAL* 2.9 7.3 + - - +
510A GLN* 1.3 73.9 - - - +
512A THR* 1.3 60.9 + - - +
514A GLN* 4.8 0.4 - - - -
515A PHE* 2.8 43.5 + - + +
519A PHE* 3.3 24.0 - - + -
585A LEU* 4.4 16.6 - - + -
587A PRO* 4.0 25.8 - - + -
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Residues in contact with THR 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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508A VAL 3.0 14.6 + - - +
509A TRP* 2.8 33.3 + - - -
511A MET* 1.3 76.1 - - - +
513A ARG* 1.3 57.4 + - - +
516A PRO* 3.0 31.5 - - - +
519A PHE* 3.4 34.7 - - + -
521A PHE* 3.8 24.0 - - + +
522A ASN 6.0 2.2 - - - +
523A GLU* 5.9 2.6 + - - +
526A LEU* 4.4 3.8 - - + -
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Residues in contact with ARG 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 TRP* 3.0 40.8 + - + +
510A GLN* 3.7 10.8 + - - +
511A MET 3.1 0.2 - - - -
512A THR* 1.3 77.2 + - - +
514A GLN* 1.3 80.1 + - - +
515A PHE 3.1 1.9 + - - -
516A PRO* 3.5 14.6 - - - +
592A SER 5.3 2.4 + - - -
593A HIS* 3.3 31.5 + - - +
594A LEU* 4.4 2.6 + - - +
595A GLU* 2.8 52.7 + - - +
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Residues in contact with GLN 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 5.7 0.4 - - - +
510A GLN* 3.0 17.8 + - - +
513A ARG* 1.3 88.6 - - - +
515A PHE* 1.3 82.6 + - + +
516A PRO* 3.4 6.5 - - - +
587A PRO* 3.3 13.8 - - - +
588A VAL* 2.7 53.1 + - - +
593A HIS* 2.9 30.0 + - + +
594A LEU* 3.9 7.7 - - - +
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Residues in contact with PHE 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A MET* 2.8 29.2 + - + +
512A THR 3.1 5.9 - - - +
514A GLN* 1.3 98.9 - - + +
516A PRO* 1.4 52.5 - - - +
517A SER 2.9 5.9 + - - -
518A ALA* 2.8 40.5 + - + +
519A PHE* 3.9 7.0 - - + -
581A GLU* 4.4 9.9 - - - +
585A LEU* 3.8 37.5 - - + -
586A TYR 3.8 12.6 - - - -
587A PRO* 3.6 40.8 - - + -
588A VAL* 6.3 0.4 - - + -
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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
------------------------------------------------------------
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