Contacts of the helix formed by residues 437 - 457 (chain A) in PDB entry 2BS3
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 THR 437 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.9 2.7 - - + -
435A LEU 3.7 0.6 + - - +
436A GLU* 1.3 71.6 - - - +
438A LYS* 1.3 56.2 + - - +
440A LEU* 3.8 12.5 - - + +
441A GLU* 2.8 43.0 + - - +
5D TYR* 4.3 28.9 - - + +
210D LYS* 4.0 9.1 - - + -
432D GLN* 2.7 22.8 + - - -
433D VAL* 2.9 39.9 + - + +
435D LEU* 4.4 12.6 - - + -
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Residues in contact with LYS 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN* 6.4 0.2 - - - -
436A GLU* 3.1 23.8 + - + -
437A THR* 1.3 77.6 + - - +
439A THR* 1.3 65.2 + - - +
441A GLU* 3.8 3.3 - - - +
442A LYS* 3.1 22.9 + - + +
432D GLN* 3.1 36.4 + - + +
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Residues in contact with THR 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ILE* 4.3 10.5 - - + -
186A HIS 4.3 8.5 - - - +
187A GLN* 2.6 35.2 + - + +
192A TYR* 5.3 3.4 - - + -
436A GLU* 3.0 17.6 + - - +
438A LYS* 1.3 81.8 - - - +
440A LEU* 1.3 67.2 + - + +
442A LYS* 3.1 14.7 + - - +
443A PHE* 3.1 51.3 + - + -
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.1 20.9 - - + -
3A VAL* 4.6 14.1 - - + -
185A ILE* 4.1 24.7 - - + -
192A TYR* 5.5 1.3 - - + -
206A ALA* 4.9 4.9 - - + -
208A VAL* 3.5 34.5 - - + -
435A LEU* 5.0 17.5 - - + -
436A GLU 3.1 17.3 + - - +
437A THR* 3.8 17.0 - - + +
439A THR* 1.3 78.2 - - + +
441A GLU* 1.3 57.4 - - - +
443A PHE* 3.3 4.3 + - - +
444A VAL* 2.9 33.5 + - - +
5D TYR* 5.8 2.5 - - + -
435D LEU* 5.9 3.4 - - + -
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Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.6 30.0 - - + +
437A THR* 2.8 21.7 + - - +
438A LYS* 3.8 4.0 - - - +
440A LEU* 1.3 78.4 - - - +
442A LYS* 1.3 55.3 + - - +
444A VAL* 4.6 0.9 - - - +
445A LYS* 2.8 52.9 + - + +
7D ASP* 5.1 1.2 - - - +
210D LYS* 2.8 36.9 + - - +
429D ALA 5.3 1.2 - - - +
432D GLN* 3.2 21.2 + - - +
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Residues in contact with LYS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A HIS 5.4 1.4 + - - -
187A GLN* 6.2 2.0 - - - +
438A LYS* 3.1 16.0 + - + +
439A THR* 3.1 16.1 + - - +
441A GLU* 1.3 75.9 - - - +
443A PHE* 1.3 87.1 + - - +
445A LYS* 4.1 3.5 - - - +
446A GLY* 2.8 27.5 + - - -
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Residues in contact with PHE 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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183A ALA* 5.1 6.5 - - + -
184A LEU 3.3 24.7 - - - -
185A ILE* 4.1 14.4 - - + -
186A HIS* 3.5 48.7 - + - -
195A VAL* 3.7 19.5 - - + -
439A THR* 3.1 35.7 + - + +
440A LEU 3.9 5.6 - - - +
442A LYS* 1.3 98.4 - - - +
444A VAL* 1.3 64.2 + - - +
446A GLY* 3.3 1.5 + - - -
447A GLN* 3.1 30.7 + - - +
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Residues in contact with VAL 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.2 24.2 - - + -
2A LYS 5.8 0.2 - - - +
195A VAL* 4.5 8.1 - - + -
204A ILE* 3.9 26.4 - - + +
205A ILE 4.7 1.8 - - - -
206A ALA* 3.5 36.3 - - + +
440A LEU 2.9 20.5 + - - +
441A GLU* 4.1 2.0 - - - +
443A PHE* 1.3 74.4 - - - +
445A LYS* 1.3 66.0 + - + +
447A GLN* 3.2 4.5 + - - +
448A GLU* 3.0 37.2 + - - +
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Residues in contact with LYS 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLU* 2.8 43.7 + - + +
442A LYS* 4.1 3.4 - - - +
444A VAL* 1.3 74.3 - - + +
446A GLY* 1.3 62.6 + - - +
448A GLU* 3.8 17.0 - - - +
449A ALA* 2.9 25.6 + - - +
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Residues in contact with GLY 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LYS 2.8 20.2 + - - -
443A PHE* 3.8 2.2 - - - -
444A VAL 3.2 0.2 - - - -
445A LYS* 1.3 78.1 - - - +
447A GLN* 1.3 61.9 + - - +
449A ALA* 3.5 6.5 + - - +
450A TYR* 3.1 25.5 + - - +
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Residues in contact with GLN 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 3.5 29.2 + - + +
183A ALA* 4.0 20.4 - - + +
195A VAL* 3.6 29.4 - - + -
204A ILE* 4.2 4.7 - - + -
443A PHE* 3.1 18.6 + - + +
444A VAL 3.2 3.3 + - - +
446A GLY* 1.3 77.9 + - - +
448A GLU* 1.3 61.1 + - - +
449A ALA 3.2 0.4 - - - -
450A TYR* 3.2 27.2 + - - +
451A MET* 2.9 34.9 + - - +
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Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 4.2 16.8 + - - -
204A ILE* 3.7 26.8 + - + +
444A VAL* 3.0 29.5 + - - +
445A LYS* 3.3 21.8 + - - +
447A GLN* 1.3 76.3 - - - +
449A ALA* 1.3 61.9 + - - +
451A MET* 3.4 5.2 + - - +
452A LYS* 3.0 23.0 + - - +
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LYS 2.9 17.5 + - - +
446A GLY* 3.6 7.0 - - - +
448A GLU* 1.3 75.4 - - - +
450A TYR* 1.3 60.3 + - - +
452A LYS* 3.2 14.5 + - - +
453A SER* 2.9 30.4 + - - -
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Residues in contact with TYR 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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446A GLY 3.1 15.5 + - - +
447A GLN* 3.2 27.1 + - - +
449A ALA* 1.3 74.4 - - - +
451A MET* 1.3 81.7 + - + +
453A SER* 2.7 28.2 + - - -
454A LEU* 3.1 35.4 + - + +
520A ALA 4.3 4.5 + - - -
521A TYR* 3.8 32.5 + - + -
524A PRO* 4.3 12.5 - - - +
525A MET* 5.6 5.8 - - + -
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Residues in contact with MET 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE* 4.3 15.7 - - + -
197A ARG* 3.9 20.9 - - - +
202A GLY 5.8 0.4 - - - +
204A ILE* 4.0 21.1 - - + -
447A GLN 2.9 20.7 + - - +
448A GLU* 3.7 5.8 - - - +
450A TYR* 1.3 107.7 - - + +
452A LYS* 1.3 63.0 + - - +
454A LEU* 3.3 8.8 + - + +
455A VAL* 3.1 26.0 + - - +
511A LEU* 4.4 17.9 - - + -
517A LEU* 4.3 9.5 - - + +
521A TYR* 3.7 35.2 - - + -
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Residues in contact with LYS 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 GLU 3.0 14.5 + - - +
449A ALA* 3.5 15.3 - - - +
450A TYR 3.2 0.2 - - - -
451A MET* 1.3 76.7 - - - +
453A SER* 1.3 56.6 + - - +
455A VAL* 3.3 7.0 + - + +
456A GLU* 2.9 73.1 + - + +
511A LEU* 5.0 5.8 - - + +
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Residues in contact with SER 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ALA 2.9 13.7 + - - -
450A TYR* 2.7 33.3 + - - -
452A LYS* 1.3 77.3 - - - +
454A LEU* 1.3 58.6 + - - +
456A GLU* 3.6 7.1 + - - +
457A SER* 2.8 31.7 + - - -
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Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A TYR* 3.1 38.2 + - + +
451A MET* 3.6 12.8 - - + +
453A SER* 1.3 83.1 + - - +
455A VAL* 1.3 63.7 + - - +
456A GLU 3.4 0.3 + - - -
457A SER* 3.5 17.5 + - - +
504A VAL* 4.9 7.4 - - + +
506A ILE* 4.0 16.9 + - + +
517A LEU* 3.9 24.5 - - + -
520A ALA* 4.1 20.6 - - + +
521A TYR* 3.8 33.2 - - + +
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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
----------------------------------------------------------
451A MET 3.1 16.5 + - - +
452A LYS* 3.7 7.4 - - + +
454A LEU* 1.3 82.5 - - - +
456A GLU* 1.3 62.8 + - + +
457A SER 3.8 0.5 + - - +
506A ILE* 4.2 19.4 - - + +
509A LYS* 2.7 78.5 + - + +
510A ARG 4.2 6.3 - - - +
511A LEU* 4.0 17.5 - - + -
517A LEU* 4.3 8.5 - - + -
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Residues in contact with GLU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LYS* 2.9 58.0 + - + +
453A SER* 3.6 5.1 - - - +
455A VAL* 1.3 83.1 - - + +
457A SER* 1.3 68.1 + - - +
458A LYS* 3.4 16.1 + - - +
509A LYS* 5.1 0.4 - - - -
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Residues in contact with SER 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A SER 2.8 16.9 + - - -
454A LEU* 3.6 13.3 - - - +
455A VAL 3.5 3.5 - - - +
456A GLU* 1.3 79.7 - - - +
458A LYS* 1.3 58.5 + - - +
459A GLY* 3.1 13.0 + - - -
502A LYS 4.9 3.6 + - - -
503A ASN* 4.6 1.2 - - - -
504A VAL 2.7 29.2 + - - -
505A GLY* 4.4 9.1 - - - -
506A ILE 5.0 0.7 + - - -
509A LYS* 5.0 6.9 + - - -
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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