Contacts of the helix formed by residues 440 - 454 (chain A) in PDB entry 6XYY
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 PHE 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A SER* 4.2 9.6 - - - -
264A SER* 3.5 23.3 - - - +
266A THR* 5.2 0.2 + - - -
269A ALA* 5.5 0.9 - - - -
271A TRP* 3.5 31.0 - + - -
328A LEU* 3.7 26.5 - - + -
363A ASN* 3.7 4.9 - - - +
367A GLU* 3.9 38.1 - - + -
368A GLY* 5.5 0.4 - - - -
371A PHE* 3.5 38.8 - + - -
435A VAL 5.3 0.2 - - - -
436A GLY* 2.9 15.2 + - - +
438A HIS 3.6 0.8 - - - -
439A PHE* 1.3 86.5 - - + +
441A THR* 1.3 66.4 + - - +
442A CYS 3.4 1.8 - - - -
443A PRO* 3.3 4.6 - - - +
444A THR* 2.9 26.1 + - - -
480A HIS* 5.7 2.9 - - + -
601A PPI 4.3 1.3 - - + -
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Residues in contact with THR 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ASN* 3.3 27.1 + - + +
364A VAL 4.3 3.1 + - - -
365A ARG 5.7 0.2 + - - -
367A GLU* 3.6 21.3 - - - +
436A GLY 3.1 10.3 + - - -
437A ASP* 4.4 13.7 + - - +
440A PHE* 1.3 76.0 - - - +
442A CYS* 1.3 59.8 + - - +
444A THR* 3.3 4.2 + - - -
445A ASN* 2.8 25.3 + - - +
460A TYR* 3.7 4.2 + - - +
462A TYR* 4.8 4.3 + - + +
556A LEU* 3.8 30.1 - - + -
559A ARG* 5.8 1.9 + - - +
560A CYS* 4.4 7.6 - - - -
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Residues in contact with CYS 442 (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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437A ASP* 3.0 30.2 + - - +
441A THR* 1.3 75.9 - - - +
443A PRO* 1.4 60.9 - - + +
445A ASN* 4.0 0.4 - - - -
446A GLU* 2.9 26.2 + - - +
559A ARG* 4.2 1.8 - - - -
560A CYS* 2.0 60.3 - - + -
563A TRP* 4.0 21.1 - - + -
564A ASN* 3.3 20.5 + - - +
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Residues in contact with PRO 443 (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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266A THR* 3.6 4.7 + - - +
268A ASN* 2.9 31.7 + - - +
269A ALA* 3.8 32.1 - - + +
270A PRO* 4.3 3.8 - - + -
437A ASP 3.5 4.9 - - - +
438A HIS 3.2 27.4 - - - +
439A PHE 3.8 11.7 - - - +
440A PHE 3.3 10.1 - - - +
442A CYS* 1.4 88.1 - - + +
444A THR* 1.3 60.9 + - - +
446A GLU* 3.4 2.3 + - + +
447A TYR 3.1 10.6 + - - -
564A ASN* 5.3 0.9 - - - +
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Residues in contact with THR 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A MET 5.5 0.9 - - - +
265A GLY* 4.2 13.6 + - - +
266A THR* 3.7 15.6 + - + +
361A MET* 3.5 25.7 - - + +
362A GLY 4.1 9.4 + - - +
363A ASN* 3.3 19.8 + - - +
440A PHE 2.9 15.1 + - - -
441A THR 3.4 8.7 - - - -
443A PRO* 1.3 72.7 - - - +
445A ASN* 1.3 66.7 + - - +
447A TYR* 3.2 1.6 + - - -
448A ALA* 2.9 22.0 + - - +
460A TYR* 3.4 21.1 - - + +
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Residues in contact with ASN 445 (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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441A THR* 2.8 20.5 + - - +
442A CYS 3.3 5.6 + - - +
444A THR* 1.3 73.9 - - - +
446A GLU* 1.3 62.8 + - - +
448A ALA* 3.2 2.4 + - - +
449A GLN* 2.5 55.8 + - - +
460A TYR* 3.6 21.4 + - - -
532A PHE* 3.9 19.9 - - - -
537A PRO* 5.6 2.6 - - - +
556A LEU* 4.4 22.8 - - - +
557A ALA* 5.5 3.7 - - - +
560A CYS* 4.0 23.3 - - - +
564A ASN* 4.2 2.0 + - - +
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Residues in contact with GLU 446 (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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268A ASN* 3.5 6.0 + - - +
346A MET* 3.1 34.7 - - - +
442A CYS 2.9 16.9 + - - +
443A PRO* 3.8 4.5 - - + +
444A THR 3.2 0.4 - - - -
445A ASN* 1.3 75.6 - - - +
447A TYR* 1.3 59.1 + - - +
449A GLN* 3.2 12.3 + - + +
450A ALA* 2.9 28.1 + - + +
564A ASN* 4.0 37.0 - - + +
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Residues in contact with TYR 447 (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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245A ASN* 3.1 44.2 + - - -
249A MET* 3.7 21.1 - - + +
262A MET* 4.6 4.7 - - + -
266A THR* 4.0 17.7 - - + -
267A MET* 6.1 0.7 - - + -
268A ASN* 3.9 19.6 - - + +
345A PRO 4.6 6.5 - - - -
348A LEU* 4.5 7.2 - - + +
349A MET* 3.9 36.2 - - + -
361A MET* 4.5 1.1 - - + -
443A PRO 3.1 14.7 + - - +
444A THR 3.8 2.9 - - - +
446A GLU* 1.3 74.6 - - - +
448A ALA* 1.3 55.3 + - - +
450A ALA* 3.0 4.6 + - + +
451A LEU* 2.7 73.2 + - + +
454A ARG* 4.6 3.3 + - - -
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A MET* 3.7 25.9 - - - +
444A THR 2.9 17.4 + - - +
445A ASN 3.5 4.9 - - - +
447A TYR* 1.3 76.8 - - - +
449A GLN* 1.3 61.8 + - - +
451A LEU* 3.3 3.2 + - - +
452A ALA* 3.1 25.6 + - - +
458A VAL* 4.2 5.5 - - + +
460A TYR* 3.8 15.5 - - + -
532A PHE* 3.5 21.4 - - + -
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Residues in contact with GLN 449 (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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445A ASN* 2.5 45.6 + - - +
446A GLU* 3.5 11.4 - - + +
448A ALA* 1.3 76.1 - - - +
450A ALA* 1.3 62.7 + - - +
452A ALA* 3.5 1.8 + - - +
453A GLU* 3.0 29.8 + - + +
532A PHE* 3.7 18.5 - - + -
534A LYS* 3.1 49.5 + - + +
537A PRO* 5.7 2.8 - - - +
564A ASN* 4.8 6.3 - - - +
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Residues in contact with ALA 450 (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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349A MET* 3.6 36.1 - - + -
446A GLU* 2.9 14.4 + - + +
447A TYR* 3.0 12.5 + - + +
449A GLN* 1.3 78.1 - - - +
451A LEU* 1.3 62.4 + - - +
453A GLU* 3.3 12.0 + - - +
454A ARG* 3.3 24.4 + - - +
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Residues in contact with LEU 451 (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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249A MET* 3.8 21.3 - - + -
262A MET* 4.3 11.0 - - + -
354A LEU* 3.4 26.4 - - + +
359A ILE* 4.3 10.3 - - + -
361A MET* 4.1 21.3 - - - -
447A TYR* 2.7 57.5 + - + +
448A ALA* 3.9 1.1 - - - +
450A ALA* 1.3 72.0 - - - +
452A ALA* 1.3 63.1 + - - +
454A ARG* 2.9 19.3 + - - +
455A GLY 3.2 8.0 + - - -
456A ALA* 3.3 16.0 + - + +
458A VAL* 3.8 12.8 - - + -
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Residues in contact with ALA 452 (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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448A ALA 3.1 16.1 + - - +
449A GLN 4.1 2.7 - - - +
451A LEU* 1.3 76.2 - - - +
453A GLU* 1.3 61.8 + - - +
455A GLY* 3.3 11.4 + - - -
456A ALA 3.8 14.8 - - - +
458A VAL* 3.8 7.2 - - + +
532A PHE 3.3 26.7 - - - +
533A SER* 4.0 15.5 - - - -
534A LYS 5.1 0.7 - - - +
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Residues in contact with GLU 453 (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 GLN 3.0 28.4 + - - +
450A ALA* 3.6 8.3 - - - +
451A LEU 3.1 0.4 - - - -
452A ALA* 1.3 79.4 - - - +
454A ARG* 1.3 61.1 + - + +
455A GLY 3.3 0.7 + - - -
534A LYS* 3.8 27.1 - - + +
535A GLU* 3.0 28.1 - - - +
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Residues in contact with ARG 454 (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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249A MET* 4.3 9.1 - - - +
254A ARG* 4.5 5.5 - - - +
348A LEU* 4.6 1.8 + - - +
349A MET* 3.0 51.0 + - + +
352A ALA* 2.9 53.4 + - - +
353A ASP* 3.4 17.5 - - - +
354A LEU* 2.8 63.1 + - + +
447A TYR* 4.6 2.8 + - - -
450A ALA 3.3 18.8 - - - +
451A LEU* 2.9 15.9 + - - +
453A GLU* 1.3 80.1 - - + +
455A GLY* 1.3 56.4 + - - +
456A ALA 3.6 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
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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