Contacts of the helix formed by residues 432 - 446 (chain B) in PDB entry 2D2O
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 ASN 432 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426B LEU* 4.2 1.1 - - - -
429B CYS* 3.1 21.7 + - - +
430B GLY 3.2 2.4 + - - +
431B GLY* 1.3 74.4 - - - +
433B GLU* 1.3 60.2 + - - +
434B ALA* 2.9 25.1 + - - +
435B LYS* 3.0 41.3 + - + +
436B PHE* 3.1 20.6 + - - +
576B TYR* 4.9 6.1 - - - -
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Residues in contact with GLU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B LEU* 4.4 7.4 - - + -
431B GLY 3.2 8.2 + - - +
432B ASN* 1.3 70.6 + - - +
434B ALA* 1.3 59.5 + - - +
436B PHE* 4.1 9.4 - - + -
437B ARG* 2.7 81.0 + - + +
480B ASN* 3.2 26.7 + - - +
483B LEU* 4.4 6.5 - - + +
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Residues in contact with ALA 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B ASN* 2.9 10.6 + - - +
433B GLU* 1.3 78.3 - - - +
435B LYS* 1.3 62.0 + - - +
437B ARG* 3.9 6.6 - - - +
438B LEU* 3.2 21.3 + - - +
575B PRO 5.5 0.7 - - - +
576B TYR* 3.8 36.8 - - + +
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Residues in contact with LYS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B PHE* 3.6 29.3 - - - +
385B ALA 4.5 12.2 + - - +
386B THR 6.1 1.0 - - - -
429B CYS* 4.1 12.8 + - + +
432B ASN* 3.0 42.1 + - + +
434B ALA* 1.3 73.2 - - - +
436B PHE* 1.3 65.4 + - - +
438B LEU* 3.3 5.3 + - - +
439B ALA* 3.1 22.3 + - - +
534B ASN* 5.4 1.6 - - - +
576B TYR* 3.4 40.2 - - + -
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Residues in contact with PHE 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LEU* 4.6 3.1 - - + -
425B PHE* 3.6 23.8 - + + -
426B LEU* 3.6 44.9 - - + -
429B CYS* 3.8 10.0 - - - -
432B ASN 3.1 12.6 + - - +
433B GLU* 3.5 13.2 - - + +
435B LYS* 1.3 79.5 - - - +
437B ARG* 1.3 66.1 + - + +
439B ALA* 3.2 5.9 + - - +
440B VAL* 3.0 41.0 + - + +
456B ASP* 3.7 26.0 - - + -
459B GLY* 6.2 0.4 - - - -
460B MET 5.8 0.4 - - - -
483B LEU* 3.8 31.9 - - + -
487B TYR* 3.6 19.5 - - - -
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Residues in contact with ARG 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B GLU* 2.7 51.2 + - + +
434B ALA* 3.9 6.1 - - - +
435B LYS 3.3 0.2 - - - -
436B PHE* 1.3 77.7 - - + +
438B LEU* 1.3 61.2 + - - +
440B VAL* 3.1 4.7 + - - +
441B LEU* 2.8 27.0 + - - +
480B ASN* 4.2 1.8 + - - -
482B GLY* 3.6 8.7 + - - -
483B LEU* 3.4 44.1 - - + +
486B PHE* 3.6 48.7 - - + +
576B TYR 6.1 0.2 - - - +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B PHE* 3.7 15.6 - - + -
434B ALA 3.2 10.2 + - - +
435B LYS* 3.7 9.6 - - - +
436B PHE 3.3 0.2 - - - -
437B ARG* 1.3 77.8 - - - +
439B ALA* 1.3 62.1 + - - +
441B LEU* 3.2 6.4 + - + +
442B PHE* 3.0 22.7 + - - +
532B LEU* 3.7 31.4 - - + -
533B ASN 3.8 7.0 - - - +
534B ASN* 3.5 44.6 - - + +
576B TYR* 3.4 27.3 + - + +
577B GLN 4.1 6.7 - - - +
578B GLY* 4.3 6.1 - - - +
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Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B VAL* 4.1 4.9 - - + +
384B PHE* 3.9 24.8 - - + -
417B LEU* 4.5 6.7 - - + +
425B PHE* 3.3 40.2 - - + -
435B LYS 3.1 6.8 + - - +
436B PHE 3.3 5.2 - - - +
438B LEU* 1.3 79.3 - - - +
440B VAL* 1.3 56.6 + - - +
442B PHE* 3.1 6.8 + - - +
443B GLN* 2.8 28.2 + - - +
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Residues in contact with VAL 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LEU* 3.9 12.8 - - + -
436B PHE* 3.0 32.7 + - + +
437B ARG* 3.5 9.2 - - - +
439B ALA* 1.3 73.5 - - - +
441B LEU* 1.3 66.9 + - - +
443B GLN* 3.2 10.8 + - - +
444B MET* 2.9 28.8 + - + +
486B PHE* 4.4 3.6 - - + -
487B TYR* 3.4 48.0 - - + +
490B LEU* 3.7 17.7 - - + -
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B ARG 2.8 13.7 + - - +
438B LEU* 3.2 12.5 + - + +
440B VAL* 1.3 77.1 - - - +
442B PHE* 1.3 58.4 + - - +
444B MET* 3.4 1.6 + - - +
445B THR* 2.8 29.8 + - - +
486B PHE* 4.3 15.3 - - + -
490B LEU* 3.7 20.4 - - + +
530B VAL* 3.8 15.7 - - + -
532B LEU* 3.6 24.9 - - + -
557B LEU* 3.6 27.8 - - + -
578B GLY* 3.8 22.4 - - - +
580B ILE* 4.3 10.8 - - + -
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Residues in contact with PHE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B PHE* 3.4 28.5 - + - -
380B VAL* 3.8 9.9 - - + -
384B PHE* 3.8 23.3 - + + -
394B PHE* 3.6 23.3 - + - -
398B LEU* 3.7 10.8 - - + -
438B LEU 3.0 12.6 + - - +
439B ALA 3.1 8.7 + - - +
441B LEU* 1.3 75.5 - - - +
443B GLN* 1.3 66.3 + - - +
445B THR* 3.1 5.5 + - - -
446B TYR* 2.9 63.5 + + - +
517B TYR* 4.0 13.9 - + - -
519B PHE* 3.8 21.8 - + - -
532B LEU* 3.8 16.4 - - + -
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Residues in contact with GLN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B PHE* 4.1 22.3 - - + -
415B ASN* 2.8 31.3 + - + +
416B LEU* 4.0 1.0 - - - +
417B LEU* 3.8 34.7 - - + +
439B ALA 2.8 13.6 + - - +
440B VAL* 3.5 10.9 - - - +
442B PHE* 1.3 79.2 - - - +
444B MET* 1.3 73.8 + - + +
445B THR 3.5 0.3 + - - -
446B TYR* 3.9 8.3 + - - +
448B GLY 5.6 0.2 - - - +
450B PRO* 3.7 26.3 - - + +
451B LEU 3.1 24.2 + - - +
452B ILE* 5.0 1.0 - - - +
487B TYR* 4.8 3.5 + - - -
494B ARG* 4.3 3.8 + - - -
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Residues in contact with MET 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B VAL* 5.0 0.9 - - + -
440B VAL* 2.9 19.3 + - + +
441B LEU 3.9 4.5 - - - +
442B PHE 3.2 0.4 - - - -
443B GLN* 1.3 97.0 - - - +
445B THR* 1.3 57.8 + - + +
450B PRO* 3.9 27.4 - - + -
452B ILE* 4.0 26.7 - - + -
487B TYR* 4.1 14.6 - - + -
490B LEU* 3.7 40.0 - - + +
491B ILE* 4.1 19.1 - - + -
494B ARG* 2.7 39.9 + - - +
500B LEU* 4.5 1.7 - - - +
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Residues in contact with THR 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B LEU* 2.8 19.6 + - + +
442B PHE* 3.1 5.9 + - - -
444B MET* 1.3 82.0 - - + +
446B TYR* 1.3 62.3 + - - +
490B LEU* 5.3 0.9 - - + -
494B ARG* 3.9 1.3 - - - +
500B LEU* 3.8 20.0 - - + +
519B PHE* 3.4 23.0 - - - -
521B ARG* 2.9 22.7 + - - +
530B VAL* 3.7 25.6 - - + +
580B ILE* 3.8 28.9 - - + -
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Residues in contact with TYR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B PHE* 3.9 30.5 - + + -
398B LEU* 3.6 40.7 + - + +
402B ARG* 4.7 14.0 + - - +
415B ASN* 4.1 2.2 + - - +
442B PHE* 2.9 45.6 + + + +
443B GLN 3.9 6.0 + - - +
444B MET 3.8 0.2 - - - -
445B THR* 1.3 82.7 + - - +
447B LEU* 1.3 97.7 + - + +
448B GLY 3.2 4.3 + - - +
494B ARG* 3.6 12.5 + - - -
505B VAL* 4.1 18.5 - - + +
517B TYR* 4.5 7.0 - - - -
519B PHE* 4.1 14.4 - + - -
521B ARG* 3.4 6.2 + - - -
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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