Contacts of the helix formed by residues 446 - 464 (chain A) in PDB entry 3RS9
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 SER 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A GLY 3.6 2.6 + - - -
445A LEU* 1.3 73.4 - - - +
447A PRO* 1.3 70.1 - - - +
448A LEU* 3.6 6.8 + - - +
449A GLU* 3.0 44.3 + - - +
450A ALA* 2.7 30.2 + - - +
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Residues in contact with PRO 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A PRO* 5.5 2.5 - - + -
360A PRO* 3.8 30.5 - - + -
361A ALA 4.8 3.4 - - - +
362A VAL* 3.6 20.0 - - + +
398A VAL* 3.9 12.1 - - + -
441A ILE* 4.0 24.2 - - + -
445A LEU 3.7 1.7 - - - +
446A SER* 1.3 86.2 - - - +
448A LEU* 1.3 54.5 + - - +
450A ALA* 3.6 1.7 + - - +
451A SER* 2.7 38.3 + - - -
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Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A VAL* 3.7 17.8 - - + +
408A VAL* 3.7 26.9 - - + -
409A THR* 4.2 1.3 - - - -
410A ASP* 3.6 44.6 - - + +
413A LYS* 3.7 36.8 - - + +
415A LEU* 4.0 13.2 - - + -
446A SER* 3.2 6.5 + - - +
447A PRO* 1.3 79.5 - - - +
449A GLU* 1.3 57.1 + - + +
451A SER* 3.3 2.8 + - - -
452A THR* 2.7 36.7 + - - +
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Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU* 3.8 32.6 - - + +
444A GLY 4.8 0.9 - - - +
445A LEU* 3.7 23.0 - - + +
446A SER* 3.0 40.6 + - - +
448A LEU* 1.3 75.1 - - + +
450A ALA* 1.3 66.4 + - - +
452A THR* 3.2 7.6 + - - -
453A VAL* 3.1 27.9 + - - +
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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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437A ILE* 3.7 7.2 - - + +
440A PHE* 3.7 25.1 - - + -
441A ILE* 3.5 28.9 - - + +
445A LEU* 3.8 7.0 - - + +
446A SER 2.7 20.8 + - - +
447A PRO 3.8 2.0 - - - +
449A GLU* 1.3 72.8 - - - +
451A SER* 1.3 55.8 + - - +
453A VAL* 3.7 1.6 + - - +
454A SER* 2.7 37.7 + - - -
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Residues in contact with SER 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A VAL* 3.4 25.8 - - - +
398A VAL* 3.8 3.5 - - - +
400A VAL* 3.6 22.9 - - - -
408A VAL* 3.8 11.0 - - - -
437A ILE* 3.9 12.4 - - - +
447A PRO 2.7 22.7 + - - -
448A LEU 3.7 4.0 - - - -
449A GLU 3.2 0.2 - - - -
450A ALA* 1.3 76.5 - - - +
452A THR* 1.3 62.5 + - - +
454A SER* 3.9 0.3 - - - -
455A VAL* 3.0 31.3 + - - +
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Residues in contact with THR 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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211A ILE* 3.7 38.8 - - + +
215A MET* 4.1 15.0 - - + -
216A VAL* 4.9 1.1 - - + -
219A LEU* 4.1 13.5 - - + -
408A VAL* 4.2 3.3 - - - +
415A LEU* 3.6 23.7 - - + +
448A LEU* 2.7 23.2 + - - +
449A GLU* 3.2 8.6 + - - -
451A SER* 1.3 76.7 - - - +
453A VAL* 1.3 62.9 + - - +
455A VAL* 3.4 5.1 - - - +
456A TYR* 3.3 22.9 + - - +
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Residues in contact with VAL 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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216A VAL* 4.2 22.2 - - + +
219A LEU* 3.6 36.8 - - + -
220A LEU* 4.2 7.9 - - + -
440A PHE* 3.5 36.6 - - + -
445A LEU* 3.9 9.6 - - + -
449A GLU 3.1 14.4 + - - +
450A ALA 4.1 2.7 - - - +
452A THR* 1.3 79.6 - - - +
454A SER* 1.3 57.8 + - - +
456A TYR* 3.5 2.1 + - - +
457A LEU* 3.1 39.0 + - + +
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Residues in contact with SER 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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433A LEU* 3.7 4.9 - - - -
436A MET* 3.3 20.5 - - - +
437A ILE* 3.3 32.1 + - - -
440A PHE* 3.2 20.0 - - - -
450A ALA 2.7 23.4 + - - -
451A SER 4.0 0.4 - - - -
453A VAL* 1.3 77.2 - - - +
455A VAL* 1.3 61.1 + - - +
458A HIS* 2.9 33.3 + - - +
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Residues in contact with VAL 455 (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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211A ILE* 3.7 21.1 - - + -
400A VAL* 3.8 28.9 - - + -
406A THR* 3.8 11.0 - - + -
408A VAL* 3.9 8.3 - - + -
417A ASN* 3.3 27.8 + - + +
433A LEU* 3.9 20.6 - - + -
437A ILE* 5.2 1.3 - - + -
451A SER* 3.0 21.5 + - - +
452A THR 3.4 8.3 - - - +
454A SER* 1.3 74.5 - - - +
456A TYR* 1.3 65.9 + - - +
458A HIS* 3.7 3.8 + - - +
459A GLY* 3.1 17.3 + - - -
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Residues in contact with TYR 456 (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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211A ILE* 3.8 29.8 - - + -
212A THR* 4.4 0.4 - - - -
213A ARG* 3.3 42.2 + - - +
216A VAL* 3.6 31.0 - - + -
417A ASN* 3.2 16.6 - - - +
419A THR* 2.9 43.1 + - + +
452A THR 3.3 7.5 + - - +
453A VAL 3.7 1.3 - - - +
454A SER 3.2 0.4 - - - -
455A VAL* 1.3 83.0 - - - +
457A LEU* 1.3 63.4 + - + +
460A PHE* 2.9 38.2 + + + +
488A LEU* 3.9 20.0 - - + -
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Residues in contact with LEU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 4.5 2.5 - - + -
220A LEU* 4.4 5.8 - - + -
258A VAL* 5.3 0.4 - - + -
436A MET* 3.8 13.9 - - + -
440A PHE* 3.8 18.8 - - + -
453A VAL* 3.1 38.9 + - + +
456A TYR* 1.3 82.1 - - + +
458A HIS* 1.3 56.8 + - - +
460A PHE* 3.8 4.0 - - + +
461A ALA* 2.9 32.4 + - - +
481A ILE* 5.3 2.6 - - + +
484A ALA* 3.9 32.7 - - + +
485A ILE* 3.9 17.9 - - + +
488A LEU* 3.6 30.3 - - + -
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Residues in contact with HIS 458 (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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424A LEU* 3.8 20.1 - - + +
429A SER 2.8 29.6 + - - -
432A VAL* 4.3 0.7 - - + -
433A LEU* 3.7 29.8 - - + +
436A MET* 3.7 15.8 - - - +
454A SER 2.9 20.0 + - - +
455A VAL* 3.7 5.7 + - - +
457A LEU* 1.3 77.4 - - - +
459A GLY* 1.3 61.6 + - - +
461A ALA* 4.7 2.5 - - - -
462A ALA* 3.4 17.2 + - - +
477A LEU* 3.6 33.5 - - + +
481A ILE* 5.6 0.7 - - - -
494A BA3 3.2 36.3 + - - -
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Residues in contact with GLY 459 (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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417A ASN* 5.0 0.2 - - - -
419A THR* 3.2 14.8 - - - -
420A GLY* 3.2 33.6 + - - -
424A LEU* 4.0 7.6 - - - -
455A VAL 3.1 10.0 + - - -
458A HIS* 1.3 81.5 + - - +
460A PHE* 1.3 60.8 + - - +
462A ALA* 3.2 10.0 + - - +
463A GLU* 3.2 9.4 + - - +
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Residues in contact with PHE 460 (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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213A ARG* 3.8 26.2 - - - -
419A THR* 3.4 9.9 + - + -
456A TYR* 2.9 40.2 + + + +
457A LEU* 3.8 7.2 - - + +
459A GLY* 1.3 73.2 - - - +
461A ALA* 1.3 65.1 + - - +
463A GLU* 3.1 28.2 + - + +
464A LEU* 3.2 24.6 + - + +
484A ALA* 3.6 38.4 - - + -
487A ARG* 3.7 30.5 - - + -
488A LEU* 4.4 4.0 - - + -
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Residues in contact with ALA 461 (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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457A LEU 2.9 22.0 + - - +
458A HIS 3.8 0.7 - - - +
460A PHE* 1.3 72.8 - - - +
462A ALA* 1.3 60.8 + - - +
464A LEU* 3.0 17.6 + - - +
477A LEU* 3.8 19.1 - - + +
480A LEU* 3.4 43.7 - - + +
481A ILE* 3.9 10.8 - - + +
484A ALA* 3.8 11.9 - - + +
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Residues in contact with ALA 462 (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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421A ASN* 3.4 21.7 + - - +
424A LEU* 3.6 35.9 - - + -
458A HIS 3.4 3.5 + - - +
459A GLY 3.2 11.5 + - - +
461A ALA* 1.3 76.9 - - - +
463A GLU* 1.3 61.2 + - - +
464A LEU 3.2 1.0 + - - -
465A PHE* 3.2 20.1 + - - +
472A LEU* 3.7 22.9 - - + +
477A LEU* 3.6 2.1 - - - +
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Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ILE 4.5 1.0 - - - +
419A THR* 3.2 13.7 - - - +
420A GLY 2.6 40.9 + - - +
421A ASN* 3.7 11.0 - - + +
459A GLY 3.2 9.4 + - - +
460A PHE* 3.1 25.7 + - + +
462A ALA* 1.3 74.7 - - - +
464A LEU* 1.3 62.2 + - + +
465A PHE 3.2 5.6 + - - +
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Residues in contact with LEU 464 (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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460A PHE* 3.4 28.5 - - + +
461A ALA* 3.0 12.2 + - - +
463A GLU* 1.3 77.1 - - - +
465A PHE* 1.3 65.8 + - - +
466A GLU* 3.3 12.3 + - - +
480A LEU* 3.9 15.9 - - + +
483A GLU* 3.9 22.9 - - + +
484A ALA* 3.6 38.1 - - + +
487A ARG* 3.6 29.8 - - - +
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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