Contacts of the helix formed by residues 517 - 539 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ALA* 6.4 0.4 - - - +
229A GLY 4.1 10.3 - - - +
230A LEU* 6.0 0.4 - - - -
233A TYR* 3.7 26.2 - - + -
515A TYR* 3.2 29.5 - - + +
516A PRO* 1.3 82.1 - - - +
518A ALA* 1.3 60.6 + - - +
519A ALA 3.1 0.2 - - - -
520A ALA* 3.1 24.2 + - + +
521A PHE* 3.4 4.9 + - - +
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Residues in contact with ALA 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ALA* 5.7 0.4 - - - -
437A LEU* 4.3 24.0 - - + -
507A TYR* 5.4 8.1 - - + +
508A VAL* 6.4 0.2 - - - -
515A TYR* 3.4 33.8 - - + +
516A PRO 3.1 0.4 - - - -
517A LEU* 1.3 74.9 - - - +
519A ALA* 1.3 59.4 + - - +
520A ALA 3.2 0.2 - - - -
521A PHE* 3.0 14.0 + - + +
522A ALA* 2.9 26.2 + - - +
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Residues in contact with ALA 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 4.6 11.5 - - + +
225A MET* 4.2 27.8 - - + -
226A ALA* 4.7 2.7 - - - +
508A VAL* 5.0 19.8 - - + +
515A TYR 4.9 0.2 + - - -
516A PRO* 3.1 15.5 + - + +
518A ALA* 1.3 78.4 - - - +
520A ALA* 1.3 57.2 + - - +
522A ALA* 3.1 9.8 + - - +
523A VAL* 2.9 26.2 + - - +
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Residues in contact with ALA 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA* 3.8 31.3 - - + +
229A GLY 6.4 0.4 - - - -
230A LEU* 6.1 2.9 - - + -
516A PRO 4.3 0.4 + - - -
517A LEU* 3.1 14.7 + - + +
519A ALA* 1.3 77.6 - - - +
521A PHE* 1.3 54.8 - - - +
523A VAL* 3.0 3.4 + - - +
524A LEU* 2.7 38.3 + - - +
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Residues in contact with PHE 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ILE* 5.8 10.3 - - + -
441A GLN* 4.7 8.8 - - - +
515A TYR* 6.3 0.7 - - + -
517A LEU 3.4 4.2 + - - +
518A ALA* 3.0 20.4 + - + +
520A ALA* 1.3 78.6 - - - +
522A ALA* 1.3 57.1 + - - +
524A LEU* 4.4 6.4 - - - +
525A ASN* 3.5 18.4 + - - +
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Residues in contact with ALA 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 6.0 3.4 - - + -
504A GLN* 5.0 21.1 - - + +
507A TYR* 6.5 1.3 - - + -
508A VAL* 6.0 3.1 - - + -
518A ALA 2.9 10.6 + - - +
519A ALA* 3.1 12.9 + - - +
521A PHE* 1.3 79.1 - - - +
523A VAL* 1.3 53.5 + - - +
524A LEU 3.3 0.2 - - - -
525A ASN* 3.0 7.7 + - - +
526A ASN* 2.8 34.4 + - - +
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Residues in contact with VAL 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A THR* 5.3 10.1 - - - +
222A LEU* 4.8 15.9 - - + +
223A ILE* 5.7 1.6 - - - +
226A ALA* 5.0 7.0 - - + -
519A ALA 2.9 15.1 + - - +
520A ALA* 3.0 8.7 + - - +
522A ALA* 1.3 77.4 - - - +
524A LEU* 1.3 53.4 + - - +
526A ASN* 3.5 6.9 - - - +
527A PHE* 2.6 38.5 + - - +
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Residues in contact with LEU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A ALA 2.7 21.4 + - - +
521A PHE* 4.5 6.3 - - - +
523A VAL* 1.3 70.9 - - - +
525A ASN* 1.3 59.6 + - - +
527A PHE* 4.1 9.3 - - - +
528A THR* 3.7 14.4 + - - -
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Residues in contact with ASN 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLN* 5.0 15.3 - - + +
445A GLN* 5.9 5.6 - - + -
521A PHE 3.5 14.1 + - - +
522A ALA* 3.0 14.4 + - - +
524A LEU* 1.3 77.9 - - - +
526A ASN* 1.3 52.8 + - - +
527A PHE 3.2 0.2 - - - -
528A THR* 2.9 9.2 + - - -
529A GLU* 2.7 33.2 + - - +
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Residues in contact with ASN 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 5.8 2.0 - - + +
219A THR* 5.0 18.8 - - - -
522A ALA 2.8 18.8 + - - +
523A VAL* 2.9 7.8 + - - +
525A ASN* 1.3 73.9 - - - +
527A PHE* 1.3 55.7 + - - +
529A GLU* 3.6 10.3 - - + +
530A VAL* 2.7 36.0 + - - +
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Residues in contact with PHE 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A VAL 2.6 20.7 + - - +
524A LEU* 4.2 10.5 - - - +
526A ASN* 1.3 72.8 - - - +
528A THR* 1.3 57.3 + - - +
530A VAL* 4.4 5.7 - - - +
531A ASN* 4.1 12.3 + - - +
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Residues in contact with THR 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A LEU 3.7 9.7 + - - -
525A ASN* 2.9 12.2 + - - -
527A PHE* 1.3 77.6 - - - +
529A GLU* 1.3 54.2 + - - +
530A VAL 3.3 0.4 - - - -
531A ASN* 3.0 9.1 + - - +
532A SER* 2.6 37.0 + - - -
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Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ASN 2.7 20.1 + - - +
526A ASN* 3.0 11.8 + - + +
528A THR* 1.3 73.2 - - - +
530A VAL* 1.3 57.0 + - - +
532A SER* 4.0 8.3 - - - -
533A ASP* 2.7 38.2 + - + +
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Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TRP 5.2 2.4 - - - +
215A LEU* 6.4 2.5 - - + -
526A ASN 2.7 19.4 + - - +
527A PHE* 4.5 7.0 - - - +
529A GLU* 1.3 73.4 - - - +
531A ASN* 1.3 59.1 + - - +
533A ASP* 4.9 2.1 - - - +
534A ALA* 3.3 20.4 + - - +
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Residues in contact with ASN 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TRP 5.4 4.7 - - - -
187A TYR* 5.6 5.1 - - + +
188A THR* 5.5 10.3 - - - +
527A PHE 4.1 8.6 + - - +
528A THR* 3.0 13.8 + - - +
530A VAL* 1.3 79.9 - - - +
532A SER* 1.3 58.6 + - - +
534A ALA* 3.1 6.5 + - - +
535A LEU* 2.9 27.8 + - - +
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Residues in contact with SER 532 (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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449A SER* 4.2 25.0 - - - -
528A THR* 2.6 21.4 + - - -
529A GLU* 3.1 8.5 + - - -
531A ASN* 1.3 73.6 - - - +
533A ASP* 1.3 51.9 + - - +
535A LEU* 3.1 10.1 + - - +
536A LYS* 2.7 33.6 + - - +
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Residues in contact with ASP 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A SER* 5.7 0.2 - - - -
529A GLU* 2.7 21.2 + - + +
530A VAL* 4.9 2.2 - - - +
532A SER* 1.3 70.5 - - - +
534A ALA* 1.3 59.3 + - - +
536A LYS* 3.1 11.0 + - + +
537A MET* 2.8 28.6 + - - +
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Residues in contact with ALA 534 (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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186A TRP* 4.3 28.0 - - + +
187A TYR* 5.4 1.3 - - - +
530A VAL 3.3 16.6 + - - +
531A ASN* 3.1 12.0 + - - +
533A ASP* 1.3 78.0 - - - +
535A LEU* 1.3 63.1 + - - +
537A MET* 3.1 8.6 + - - +
538A CYS* 3.0 24.3 + - - +
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Residues in contact with LEU 535 (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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531A ASN 2.9 12.4 + - - +
532A SER* 3.1 12.1 + - - +
534A ALA* 1.3 75.7 - - - +
536A LYS* 1.3 57.1 + - - +
538A CYS* 4.2 6.7 - - - -
539A ARG* 2.9 35.2 + - + +
540A VAL* 3.6 3.9 + - - +
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Residues in contact with LYS 536 (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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449A SER* 6.0 4.7 - - - -
491A TYR* 6.5 0.2 - - + -
532A SER 2.7 17.7 + - - +
533A ASP* 3.1 15.9 + - + +
535A LEU* 1.3 72.3 - - - +
537A MET* 1.3 56.5 + - - +
540A VAL* 3.3 14.5 - - + +
541A PHE* 3.3 45.1 + - + -
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Residues in contact with MET 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PHE* 3.7 39.0 - - + -
533A ASP 2.8 15.2 + - - +
534A ALA* 3.1 8.2 + - - +
536A LYS* 1.3 77.8 - - - +
538A CYS* 1.3 59.9 + - - +
540A VAL 4.8 0.2 - - - -
541A PHE* 4.8 12.8 - - - +
542A LYS 5.5 1.2 - - - +
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Residues in contact with CYS 538 (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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179A LEU* 5.9 9.8 - - + +
183A GLU* 4.9 16.6 - - + -
534A ALA 3.0 15.2 + - - +
535A LEU* 3.8 6.7 - - - +
537A MET* 1.3 80.2 - - - +
539A ARG* 1.3 82.1 + - + +
540A VAL 3.7 0.7 - - - -
541A PHE 5.3 3.3 - - - +
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Residues in contact with ARG 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LEU 6.2 0.2 - - - -
180A LYS* 5.2 13.1 - - - +
183A GLU* 5.3 9.3 - - - +
456A GLN* 5.2 6.2 - - - +
535A LEU* 2.9 12.4 + - + +
538A CYS* 1.3 92.0 + - + +
540A VAL* 1.3 61.1 + - - +
541A 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