Contacts of the helix formed by residues 517 - 539 (chain B) in PDB entry 6R7Z
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 LEU 517 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ALA* 6.4 0.4 - - - +
229B GLY 4.1 10.5 + - - +
230B LEU* 6.0 0.4 - - - -
233B TYR* 3.7 26.2 - - + -
515B TYR* 3.2 30.6 - - + +
516B PRO* 1.3 82.2 - - - +
518B ALA* 1.3 60.0 + - - +
519B ALA 3.1 0.2 - - - -
520B ALA* 3.1 24.2 + - + +
521B PHE* 3.4 4.9 + - - +
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Residues in contact with ALA 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU 6.3 0.2 - - - -
434B ALA* 5.7 0.2 - - - -
437B LEU* 4.3 23.6 - - + -
507B TYR* 5.4 8.7 - - + +
508B VAL* 6.4 0.2 - - - -
515B TYR* 3.4 33.1 - - + +
516B PRO 3.1 0.6 - - - -
517B LEU* 1.3 74.3 - - - +
519B ALA* 1.3 61.5 + - - +
521B PHE* 3.0 14.7 + - + +
522B ALA* 2.9 25.6 + - - +
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Residues in contact with ALA 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 4.6 11.2 - - + +
225B MET* 4.2 28.0 - - + -
226B ALA* 4.7 2.2 - - - +
508B VAL* 5.0 19.6 - - + +
515B TYR 4.9 0.2 + - - -
516B PRO* 3.1 15.3 + - + +
518B ALA* 1.3 79.9 - - - +
520B ALA* 1.3 57.0 + - - +
522B ALA* 3.1 10.7 + - - +
523B VAL* 2.9 26.3 + - - +
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Residues in contact with ALA 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ALA* 3.8 30.7 - - + +
229B GLY 6.4 0.4 - - - -
230B LEU* 6.1 2.9 - - + -
516B PRO 4.3 0.6 + - - -
517B LEU* 3.1 14.5 + - - +
519B ALA* 1.3 78.1 - - - +
521B PHE* 1.3 53.9 + - - +
523B VAL* 3.0 4.5 + - - +
524B LEU* 2.7 37.4 + - - +
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Residues in contact with PHE 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ILE* 5.8 10.5 - - + -
441B GLN* 4.7 8.3 - - - +
515B TYR* 6.3 0.2 - - + -
517B LEU 3.4 4.2 + - - +
518B ALA* 3.0 20.5 + - + +
520B ALA* 1.3 77.2 - - - +
522B ALA* 1.3 58.9 + - - +
524B LEU* 4.4 6.1 - - - +
525B ASN* 3.5 18.2 + - - +
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Residues in contact with ALA 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 6.0 3.1 - - + -
504B GLN* 5.0 21.1 - - + +
507B TYR* 6.5 1.3 - - + -
508B VAL* 6.0 2.7 - - + -
518B ALA 2.9 10.8 + - - +
519B ALA* 3.1 13.2 + - - +
521B PHE* 1.3 79.0 - - - +
523B VAL* 1.3 54.7 + - - +
525B ASN* 3.0 7.7 + - - +
526B ASN* 2.8 34.1 + - - +
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Residues in contact with VAL 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B THR* 5.3 10.3 - - - +
222B LEU* 4.8 14.8 - - + +
223B ILE* 5.7 1.8 - - + +
226B ALA* 5.0 7.4 - - + -
519B ALA 2.9 15.0 + - - +
520B ALA* 3.0 8.5 + - - +
522B ALA* 1.3 77.8 - - - +
524B LEU* 1.3 52.2 + - - +
526B ASN* 2.9 8.2 + - - +
527B PHE* 2.6 37.9 + - - +
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Residues in contact with LEU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B ALA 2.7 21.9 + - - +
521B PHE* 4.4 6.1 - - - +
523B VAL* 1.3 71.6 - - - +
525B ASN* 1.3 59.2 + - - +
527B PHE* 4.1 9.5 - - - +
528B THR* 3.7 14.6 + - - -
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Residues in contact with ASN 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B GLN* 5.0 14.8 - - + +
445B GLN* 5.9 6.7 - - + -
521B PHE 3.5 15.6 + - - +
522B ALA* 3.0 13.3 + - - +
524B LEU* 1.3 77.4 - - - +
526B ASN* 1.3 53.4 + - - +
527B PHE 3.2 0.2 - - - -
528B THR* 2.9 9.3 + - - -
529B GLU* 2.7 33.9 + - - +
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Residues in contact with ASN 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 5.8 2.2 - - + +
219B THR* 5.0 18.4 - - - -
522B ALA 2.8 19.1 + - - +
523B VAL* 2.9 7.4 + - - +
525B ASN* 1.3 73.0 - - - +
527B PHE* 1.3 55.7 + - - +
529B GLU* 3.6 10.3 - - + +
530B VAL* 2.7 36.3 + - - +
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Residues in contact with PHE 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B VAL 2.6 21.0 + - - +
524B LEU* 4.2 10.3 - - - +
526B ASN* 1.3 73.2 - - - +
528B THR* 1.3 57.6 + - - +
530B VAL* 4.4 5.9 - - - +
531B ASN* 4.1 12.1 + - - +
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Residues in contact with THR 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B LEU 3.7 9.7 + - - -
525B ASN* 2.9 11.9 + - - -
527B PHE* 1.3 78.2 - - - +
529B GLU* 1.3 54.7 + - - +
530B VAL 3.3 0.4 - - - -
531B ASN* 3.0 9.5 + - - +
532B SER* 2.6 38.0 + - - -
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Residues in contact with GLU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B ASN 2.7 19.1 + - - +
526B ASN* 3.0 12.1 + - + +
528B THR* 1.3 74.8 - - - +
530B VAL* 1.3 57.4 + - - +
532B SER* 4.0 8.1 - - - -
533B ASP* 2.7 38.0 + - + +
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Residues in contact with VAL 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TRP 5.2 2.7 - - - +
215B LEU* 6.4 2.5 - - + -
526B ASN 2.7 20.9 + - - +
527B PHE* 4.5 7.0 - - - +
529B GLU* 1.3 73.3 - - - +
531B ASN* 1.3 59.1 + - - +
533B ASP* 4.9 1.7 - - - +
534B ALA* 3.3 19.6 + - - +
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Residues in contact with ASN 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TRP 5.4 4.9 - - - -
187B TYR* 5.6 5.1 - - - +
188B THR* 5.5 9.6 - - - +
527B PHE 4.1 8.1 + - - +
528B THR* 3.0 13.8 + - - +
530B VAL* 1.3 80.1 - - - +
532B SER* 1.3 58.7 + - - +
534B ALA* 3.1 7.1 + - - +
535B LEU* 2.9 27.9 + - - +
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Residues in contact with SER 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B SER* 4.2 24.4 - - - -
528B THR* 2.6 20.9 + - - -
529B GLU* 3.1 8.3 + - - -
531B ASN* 1.3 74.0 - - - +
533B ASP* 1.3 53.6 + - - +
535B LEU* 3.1 10.0 + - - +
536B LYS* 2.7 33.1 + - - +
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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
----------------------------------------------------------
449B SER* 5.7 0.2 - - - -
529B GLU* 2.7 21.2 + - + +
530B VAL* 4.9 2.2 - - - +
532B SER* 1.3 69.7 - - - +
534B ALA* 1.3 58.8 + - - +
536B LYS* 3.1 11.8 + - + +
537B MET* 2.8 28.2 + - - +
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Residues in contact with ALA 534 (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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186B TRP* 4.3 27.8 - - + +
187B TYR* 5.4 1.3 - - - +
530B VAL 3.3 16.9 + - - +
531B ASN* 3.1 12.0 + - - +
533B ASP* 1.3 77.2 - - - +
535B LEU* 1.3 62.9 + - - +
537B MET* 3.1 9.5 + - - +
538B CYS* 3.0 24.2 + - - +
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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
----------------------------------------------------------
531B ASN 2.9 12.8 + - - +
532B SER* 3.4 11.2 - - - +
534B ALA* 1.3 76.2 - - - +
536B LYS* 1.3 57.0 + - - +
538B CYS* 4.2 6.1 - - - -
539B ARG* 2.9 34.6 + - + +
540B VAL* 3.6 4.2 + - - +
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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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449B SER* 6.0 4.7 - - - -
491B TYR* 6.5 0.2 - - + -
532B SER 2.7 17.5 + - - +
533B ASP* 3.1 15.5 + - - +
535B LEU* 1.3 72.7 - - - +
537B MET* 1.3 57.1 + - - +
540B VAL* 3.3 14.5 - - + +
541B PHE* 3.3 45.3 + - + -
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Residues in contact with MET 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.7 39.6 - - + -
533B ASP 2.8 15.3 + - - +
534B ALA* 3.1 8.7 + - - +
536B LYS* 1.3 77.6 - - - +
538B CYS* 1.3 59.8 + - - +
540B VAL 4.8 0.4 - - - -
541B PHE* 4.8 12.7 - - - +
542B LYS 5.5 1.4 - - - +
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Residues in contact with CYS 538 (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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179B LEU* 5.9 9.5 - - + +
183B GLU* 4.9 16.8 - - + -
534B ALA 3.0 15.8 + - - +
535B LEU* 3.1 6.7 + - - +
537B MET* 1.3 81.4 - - - +
539B ARG* 1.3 81.7 + - + +
540B VAL 3.7 0.4 - - - -
541B PHE 5.3 2.5 - - - +
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Residues in contact with ARG 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU 6.2 0.4 - - - -
180B LYS* 5.2 12.7 - - - +
183B GLU* 5.3 9.9 - - - +
456B GLN* 5.2 6.6 - - - +
535B LEU* 2.9 12.9 + - + +
538B CYS* 1.3 91.4 + - + +
540B VAL* 1.3 61.0 + - - +
541B PHE 5.3 0.7 - - - -
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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