Contacts of the helix formed by residues 530 - 546 (chain A) in PDB entry 4Y2P
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 LYS 530 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A ARG* 3.1 16.8 - - - +
519A ILE* 3.8 27.6 - - + -
520A GLU 3.9 10.3 - - - -
521A ASP* 3.2 24.5 + - - +
522A CYS* 3.9 9.6 - - + -
526A THR 3.0 10.3 + - - +
529A ASP* 1.3 105.1 + - - +
531A PRO* 1.3 66.0 - - - +
533A GLU* 3.2 33.0 + - - +
534A VAL* 2.9 22.0 + - - +
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Residues in contact with PRO 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.0 18.4 - - + -
229A PRO* 4.0 18.4 - - + -
276A TYR* 3.6 33.9 - - + -
277A GLN* 3.8 4.3 - - - +
527A GLN 3.2 22.9 - - - +
528A MET 3.7 6.1 - - - +
529A ASP 3.3 9.4 - - - +
530A LYS* 1.3 89.5 - - - +
532A THR* 1.3 58.6 + - - +
533A GLU* 4.7 0.7 - - - +
534A VAL* 3.6 1.4 - - + +
535A ASN* 2.9 35.5 + - - -
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Residues in contact with THR 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A PRO 4.6 6.9 + - - -
228A LEU* 5.0 1.7 - - - +
229A PRO* 3.6 25.2 - - + +
530A LYS 3.3 0.4 - - - -
531A PRO* 1.3 82.2 - - - +
533A GLU* 1.3 74.5 + - + +
535A ASN* 3.5 4.0 + - - +
536A GLN* 3.1 24.7 + - + +
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Residues in contact with GLU 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ILE* 4.2 23.3 - - + -
530A LYS* 3.2 43.5 - - + +
531A PRO* 4.7 0.2 - - - +
532A THR* 1.3 83.6 + - + +
534A VAL* 1.3 68.2 + - - +
536A GLN* 3.4 12.1 + - - +
537A ILE* 3.0 32.2 + - + +
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Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLN* 3.6 22.4 - - + +
358A LEU* 4.4 16.6 - - + -
491A VAL* 6.2 0.7 - - - -
519A ILE* 3.7 11.0 - - + +
526A THR* 3.6 40.4 - - + +
527A GLN* 4.2 2.5 - - + -
530A LYS 2.9 19.6 + - - +
531A PRO 3.6 4.0 - - - +
533A GLU* 1.3 77.2 - - - +
535A ASN* 1.3 63.9 + - - +
537A ILE* 3.2 4.5 + - - +
538A LEU* 2.9 47.5 + - + +
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Residues in contact with ASN 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO* 3.5 19.5 - - + +
276A TYR 3.1 16.1 - - - +
277A GLN* 3.0 46.7 + - - +
280A ALA* 3.4 22.2 - - + +
281A LEU* 4.9 2.8 - - - +
531A PRO 2.9 17.9 + - - +
532A THR* 3.7 5.8 - - - +
534A VAL* 1.3 71.3 - - - +
536A GLN* 1.3 65.0 + - - +
538A LEU* 3.3 3.7 + - - -
539A ILE* 3.0 36.2 + - + +
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Residues in contact with GLN 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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532A THR* 3.1 16.4 + - + +
533A GLU* 3.7 16.4 - - - +
535A ASN* 1.3 79.8 - - - +
537A ILE* 1.3 80.3 + - - +
539A ILE* 4.3 4.3 - - - +
540A LYS* 3.1 44.2 + - + +
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Residues in contact with ILE 537 (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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489A LEU* 4.1 11.2 - - + -
491A VAL* 4.0 26.5 - - + -
517A GLY* 4.6 11.9 - - - -
518A HIS 4.4 16.8 - - - +
519A ILE* 3.6 31.0 - - + -
533A GLU* 3.0 25.2 + - + +
534A VAL* 3.2 4.0 + - - +
536A GLN* 1.3 96.4 - - - +
538A LEU* 1.3 64.9 + - + +
540A LYS* 3.9 9.2 - - - +
541A TRP* 3.2 22.2 + - - +
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Residues in contact with LEU 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 5.7 0.2 - - + -
274A TRP* 4.8 5.6 - - + -
277A GLN* 4.3 13.2 - - + -
281A LEU* 4.2 17.3 - - + -
332A ILE* 4.2 39.9 - - + -
356A ALA* 4.5 3.1 - - + -
358A LEU* 4.4 14.4 - - + -
489A LEU* 4.0 22.0 - - + -
534A VAL* 2.9 39.6 + - + +
535A ASN 3.9 2.2 - - - +
537A ILE* 1.3 75.7 - - + +
539A ILE* 1.3 57.5 + - - +
541A TRP* 3.5 4.5 + - + +
542A LEU* 2.7 44.2 + - + +
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Residues in contact with ILE 539 (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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280A ALA* 3.9 28.3 - - + +
281A LEU* 3.7 21.3 - - + -
284A ALA* 3.8 24.5 - - + -
535A ASN* 3.0 26.7 + - + +
536A GLN* 4.3 4.0 - - - +
538A LEU* 1.3 74.3 - - - +
540A LYS* 1.3 66.6 + - - +
542A LEU* 4.3 7.4 - - + -
543A ASP* 2.9 41.8 + - - +
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Residues in contact with LYS 540 (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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516A ARG 6.0 2.0 - - - -
536A GLN* 3.1 38.7 + - + +
537A ILE* 3.9 8.3 - - - +
539A ILE* 1.3 79.7 - - - +
541A TRP* 1.3 66.5 + - - +
543A ASP* 3.9 4.8 - - - +
544A SER* 3.1 26.5 + - - -
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Residues in contact with TRP 541 (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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330A VAL* 3.9 8.1 - - + -
332A ILE* 4.4 3.1 - - + -
354A ALA* 3.5 31.6 - - + -
355A VAL 3.3 33.0 - - - -
356A ALA* 3.6 12.8 - - + -
487A PRO* 4.0 5.2 - - + -
488A ALA 3.9 9.7 + - - +
489A LEU* 3.5 46.5 - - + +
515A LYS* 4.3 11.7 - - + -
537A ILE 3.2 15.6 + - - +
538A LEU* 4.1 6.7 - - + -
540A LYS* 1.3 83.1 - - - +
542A LEU* 1.3 93.3 + - + +
544A SER* 3.2 5.3 + - - -
545A ASP* 2.8 57.3 + - + +
546A ALA* 5.2 0.4 - - + -
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Residues in contact with LEU 542 (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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261A VAL* 4.3 12.6 - - + -
281A LEU* 4.2 26.7 - - + -
286A TYR* 3.3 42.8 + - + +
330A VAL* 3.8 18.6 - - + -
332A ILE* 4.4 6.5 - - + -
538A LEU 2.7 32.9 + - - +
539A ILE* 3.7 7.2 - - + +
541A TRP* 1.3 98.8 - - + +
543A ASP* 1.3 59.9 + - - +
546A ALA* 2.8 41.9 + - + +
547A ARG* 3.4 2.4 - - - +
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Residues in contact with ASP 543 (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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284A ALA* 4.3 6.8 - - - +
286A TYR* 2.9 27.0 + - - -
539A ILE* 2.9 39.2 + - - +
540A LYS* 3.9 4.8 - - - +
542A LEU* 1.3 75.0 - - - +
544A SER* 1.3 59.5 + - - +
547A ARG* 3.3 25.8 + - + +
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Residues in contact with SER 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A LYS* 4.1 5.8 + - - -
540A LYS* 3.1 14.6 + - - -
541A TRP* 3.2 10.0 + - - -
543A ASP* 1.3 80.2 - - - +
545A ASP* 1.3 81.8 + - - +
546A ALA 3.8 0.4 - - - -
547A ARG 4.8 3.6 + - - -
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Residues in contact with ASP 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ARG* 3.1 19.8 + - - -
354A ALA* 4.6 0.4 - - - +
487A PRO* 3.6 29.3 - - + +
488A ALA 5.2 0.3 + - - -
515A LYS* 2.7 38.6 + - - +
541A TRP* 2.8 40.7 + - + +
544A SER* 1.3 97.8 + - - +
546A ALA* 1.3 57.4 + - - +
547A ARG 3.5 3.8 - - - -
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Residues in contact with ALA 546 (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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259A PRO* 4.5 13.5 - - - +
286A TYR* 4.7 4.2 - - + -
330A VAL* 3.7 27.4 - - + -
353A ARG* 3.1 28.0 + - - +
354A ALA* 4.4 7.9 - - + -
541A TRP* 4.8 1.6 - - + +
542A LEU* 2.8 29.1 + - + +
545A ASP* 1.3 77.2 - - + +
547A ARG* 1.3 60.7 + - - +
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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