Contacts of the helix formed by residues 516 - 533 (chain B) in PDB entry 6CM9
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 516 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B SER 5.1 0.4 + - - -
478B THR* 3.9 34.8 + - - +
481B GLN* 4.2 13.6 + - - +
514B SER* 3.4 1.8 - - - -
515B ASP* 1.3 80.4 + - - +
517B PRO* 1.3 71.5 - - - +
518B ASP* 4.0 4.4 + - - +
519B LEU* 3.1 28.3 + - + +
520B ARG* 2.8 28.3 + - - +
439G PRO* 4.3 11.0 - - + +
525G TYR* 3.9 6.9 + - - -
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Residues in contact with PRO 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B ASP 3.2 10.5 - - - +
516B ASN* 1.3 84.7 - - - +
518B ASP* 1.3 60.1 + - - +
520B ARG* 3.8 9.3 - - + +
521B ASP* 2.9 35.0 + - - +
439G PRO* 4.0 13.9 - - + +
442G ILE* 3.7 31.6 - - + -
478G TRP* 3.9 25.7 + - + +
525G TYR* 3.2 24.9 - - + +
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Residues in contact with ASP 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B THR* 5.8 5.3 - - + +
482B LEU* 3.3 18.4 - - + +
516B ASN* 3.4 7.0 + - - +
517B PRO* 1.3 78.9 - - - +
519B LEU* 1.3 57.6 + - - +
521B ASP* 3.4 4.3 + - - +
522B ARG* 3.0 34.5 + - - +
521G VAL 5.5 1.8 - - - +
524G GLY* 3.4 13.9 - - - +
525G TYR* 3.4 24.7 + - + -
528G THR* 3.0 26.2 + - - +
562G ARG* 2.4 29.6 + - - -
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Residues in contact with LEU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B PHE* 3.7 26.9 - - + -
481B GLN* 3.5 46.9 - - + +
482B LEU* 4.3 10.5 - - + +
485B LEU* 3.7 21.5 - - + -
510B ALA* 3.8 10.1 - - + +
514B SER* 3.7 20.0 - - - +
516B ASN* 3.1 26.8 + - + +
518B ASP* 1.3 79.9 - - - +
520B ARG* 1.3 56.3 + - - +
522B ARG* 3.9 1.5 - - - -
523B GLY* 2.9 26.2 + - - -
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Residues in contact with ARG 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ALA 4.2 11.7 - - - +
511B THR 4.2 8.3 + - - +
514B SER 3.3 27.5 + - - +
515B ASP* 4.6 8.0 + - - +
516B ASN 2.8 17.6 + - - +
517B PRO* 3.8 8.1 - - + +
518B ASP 3.3 0.2 - - - -
519B LEU* 1.3 75.4 - - - +
521B ASP* 1.3 62.3 + - - +
523B GLY* 4.9 0.2 - - - -
524B TYR* 2.9 55.1 + - + +
443G GLN* 3.7 22.2 + - - +
446G THR* 5.3 5.5 - - - +
584G MET* 4.5 10.2 - - + +
585G PRO* 2.5 50.2 + - - +
586G VAL* 5.0 0.8 - - - +
587G MET* 3.9 19.1 - - - +
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Residues in contact with ASP 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B PRO 2.9 23.0 + - - +
518B ASP* 3.7 7.2 - - - +
519B LEU 3.3 0.2 - - - -
520B ARG* 1.3 76.2 - - - +
522B ARG* 1.3 58.2 + - + +
524B TYR* 3.5 0.9 + - - +
525B ILE* 2.9 38.9 + - + +
478G TRP* 3.3 24.5 + - - -
525G TYR* 5.3 0.9 - - - -
528G THR* 3.4 27.8 - - + +
532G LYS* 3.3 30.1 + - - -
584G MET* 3.4 19.5 - - + +
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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
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482B LEU* 3.7 13.5 - - + +
485B LEU* 3.7 18.4 - - + -
486B THR* 4.3 6.7 + - - -
518B ASP 3.0 20.7 + - - +
521B ASP* 1.3 76.4 - - - +
523B GLY* 1.3 58.0 + - - +
525B ILE* 3.8 11.3 - - - +
526B TYR* 2.4 76.1 + - + -
558G GLU* 4.1 7.2 + - - -
561G GLN* 5.2 2.0 - - - +
562G ARG* 3.3 49.3 - - - +
565G GLU* 2.6 22.2 + - - +
566G TYR* 3.6 32.3 + - - -
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Residues in contact with GLY 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B LEU* 3.5 13.2 - - - +
507B LEU* 3.5 12.1 - - - +
510B ALA* 4.9 1.6 - - - -
511B THR* 3.6 19.1 - - - -
519B LEU 2.9 18.8 + - - -
521B ASP 3.3 0.2 - - - -
522B ARG* 1.3 77.2 - - - +
524B TYR* 1.3 56.5 + - - +
526B TYR* 3.4 0.7 + - - -
527B TRP* 2.9 29.3 + - - +
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Residues in contact with TYR 524 (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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511B THR* 3.2 45.0 + - + -
520B ARG* 2.9 45.4 + - + +
523B GLY* 1.3 73.7 - - - +
525B ILE* 1.3 62.1 + - - +
527B TRP* 4.2 26.0 - + + -
528B ARG* 2.9 51.4 + - - +
584G MET* 3.6 29.8 - - + -
585G PRO* 3.3 34.9 - - + +
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Residues in contact with ILE 525 (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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521B ASP* 2.9 30.4 + - + +
522B ARG* 3.8 15.7 - - - +
524B TYR* 1.3 76.3 - - - +
526B TYR* 1.3 68.2 + - + +
528B ARG* 3.9 3.1 - - - +
529B LEU* 2.9 35.3 + - + +
528G THR* 5.4 3.4 - - + -
531G MET* 4.7 2.7 - - + -
532G LYS* 5.9 2.9 - - + +
566G TYR* 3.7 33.4 - - + +
569G LEU* 5.5 5.6 - - + -
580G LEU* 4.4 20.9 - - + +
581G LEU* 4.4 24.9 - - + -
584G MET* 5.2 5.8 - - + -
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Residues in contact with TYR 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LEU* 6.5 0.2 - - + -
485B LEU* 3.4 33.7 - - + -
486B THR* 3.8 18.3 + - - +
489B VAL* 3.6 40.6 - - + +
507B LEU* 4.5 7.9 - - + -
522B ARG* 2.4 63.9 + - - +
523B GLY 3.9 3.4 - - - +
525B ILE* 1.3 84.4 - - + +
527B TRP* 1.3 56.9 + - - +
529B LEU* 3.8 11.4 - - + +
530B LEU* 2.9 32.9 + - - +
541B VAL* 3.9 20.8 - - + +
565G GLU* 2.9 10.9 + - - -
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Residues in contact with TRP 527 (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 GLN* 4.9 12.1 + - - +
507B LEU* 3.5 34.0 - - + +
511B THR* 5.3 3.1 - - + -
523B GLY 2.9 18.7 + - - +
524B TYR* 3.9 26.9 - + + +
525B ILE 3.3 0.2 - - - -
526B TYR* 1.3 77.5 - - - +
528B ARG* 1.3 82.5 + - + +
530B LEU* 3.4 2.3 + - + +
531B SER* 2.9 48.6 + - - -
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Residues in contact with ARG 528 (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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524B TYR* 2.9 38.0 + - - +
525B ILE 4.1 0.7 - - - +
527B TRP* 1.3 91.8 - - + +
529B LEU* 1.3 59.9 + - - +
531B SER* 4.8 2.5 - - - -
532B THR* 2.3 41.3 + - - +
579G ALA 4.9 3.4 - - - +
580G LEU* 3.1 44.0 + - + +
581G LEU* 3.9 0.4 - - - +
582G GLU* 3.0 53.7 + - - +
583G ARG 3.7 12.5 + - - -
584G MET* 4.1 16.5 - - - +
585G PRO* 4.8 3.8 - - - +
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Residues in contact with LEU 529 (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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489B VAL* 6.0 1.8 - - + -
525B ILE* 2.9 22.8 + - + +
526B TYR* 3.8 14.1 - - + +
528B ARG* 1.3 78.7 - - - +
530B LEU* 1.3 58.2 + - - +
532B THR* 4.5 3.1 - - - -
533B ASP* 3.1 34.3 + - + +
534B PRO* 4.3 0.3 - - - +
536B ALA* 5.3 1.6 - - + -
537B ALA* 3.9 26.7 - - + +
540B VAL* 3.9 27.1 - - + -
541B VAL* 3.9 30.1 - - + -
569G LEU* 5.2 3.8 - - + -
576G MET* 6.2 3.8 - - + -
580G LEU* 4.7 17.4 - - + +
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Residues in contact with LEU 530 (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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489B VAL* 5.9 9.2 - - + -
492B PHE* 3.6 38.8 - - + -
493B LEU* 5.2 8.7 - - + -
503B VAL* 3.7 27.8 - - + -
504B GLN* 4.7 8.5 - - - +
507B LEU* 4.7 9.6 - - + -
526B TYR 2.9 17.8 + - - +
527B TRP* 4.0 4.5 - - + +
529B LEU* 1.3 78.9 - - + +
531B SER* 1.3 61.5 + - - +
534B PRO* 3.4 40.0 - - + +
537B ALA* 5.5 2.5 - - + -
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Residues in contact with SER 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B GLN* 5.9 1.2 + - - -
527B TRP* 2.9 43.4 + - - -
528B ARG* 4.5 2.9 - - - -
530B LEU* 1.3 77.2 - - - +
532B THR* 1.3 64.7 + - - +
534B PRO* 4.9 1.0 - - - +
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Residues in contact with THR 532 (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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528B ARG* 2.3 30.5 + - - +
529B LEU* 4.0 4.5 - - + -
530B LEU 3.3 0.2 - - - -
531B SER* 1.3 81.0 - - - +
533B ASP* 1.3 61.9 + - - +
534B PRO* 4.1 2.6 - - - +
576G MET* 3.7 27.1 - - + -
579G ALA* 4.9 16.0 + - + -
580G LEU* 5.4 6.8 - - + +
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Residues in contact with ASP 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B LEU* 3.1 14.0 + - + +
532B THR* 1.3 81.6 - - + +
534B PRO* 1.3 67.3 - - - +
535B VAL* 3.5 18.2 + - - +
536B ALA* 3.2 31.2 + - + +
537B ALA* 3.3 8.3 + - - +
573G TYR* 5.2 1.6 - - - -
576G MET* 3.8 27.0 - - + +
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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
------------------------------------------------------------
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