Contacts of the helix formed by residues 435 - 451 (chain B) in PDB entry 5AM8
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 435 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B GLN* 3.1 41.8 + - + +
260B SER* 5.2 2.5 - - - -
431B GLU 3.7 7.7 + - - +
432B LYS 3.5 11.5 + - - +
433B ILE 3.1 0.8 - - - -
434B ALA* 1.3 79.0 - - - +
436B LEU* 1.3 62.9 + - + +
437B PRO 3.4 0.2 - - - -
438B PHE* 2.9 14.2 + + - +
439B GLY* 2.8 41.5 + - - -
498B TYR* 3.4 33.7 - + - -
501B TYR* 3.6 37.2 - + + -
502B PHE* 4.4 0.7 - - - -
505B PHE* 3.4 40.4 - + + -
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TYR* 4.1 11.7 - - + -
218B LEU* 3.9 40.6 - - + +
222B TYR* 5.9 1.8 - - + -
432B LYS 3.6 11.0 - - - +
433B ILE* 3.5 29.2 - - + +
435B PHE* 1.3 78.1 - - + +
437B PRO* 1.4 70.7 - - + +
439B GLY 3.3 0.5 + - - -
440B TYR* 3.0 25.3 + - - +
502B PHE* 3.5 23.8 - - + -
505B PHE* 3.9 28.7 - - + -
506B VAL* 4.9 3.6 - - + -
570B LEU* 4.5 10.1 - - + -
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Residues in contact with PRO 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TYR* 3.3 28.7 - - + +
222B TYR* 3.6 27.8 - - + -
433B ILE 3.6 6.3 - - - +
434B ALA 3.4 15.9 - - - +
436B LEU* 1.4 94.1 - - + +
438B PHE* 1.3 57.5 + - - +
440B TYR* 3.4 2.6 + - + +
441B LEU* 2.9 33.9 + - - +
470B TYR* 3.5 28.0 - - + +
471B GLN* 3.9 6.3 - - + -
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Residues in contact with PHE 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TRP* 4.0 12.8 - + + -
259B GLN* 3.6 31.6 - - + +
434B ALA 5.0 0.2 - - - +
435B PHE* 2.9 13.9 + + - +
437B PRO* 1.3 77.1 - - - +
439B GLY* 1.3 66.7 + - - +
440B TYR 3.1 0.7 + - - -
441B LEU* 3.2 17.5 + - + -
442B VAL* 3.3 36.8 + - + +
463B TRP* 4.2 13.0 - + - -
467B ARG* 3.5 19.1 - - - -
471B GLN* 3.3 30.5 - - - +
489B LYS* 4.0 23.6 - - + -
498B TYR* 3.4 31.9 - + - -
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Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B PHE* 2.8 39.1 + - - -
436B LEU 3.8 2.5 - - - -
438B PHE* 1.3 77.5 - - - +
440B TYR* 1.3 60.0 + - - +
442B VAL 4.5 1.0 + - - -
443B ASP 5.0 0.9 + - - -
498B TYR* 3.8 22.1 - - - +
499B ILE* 4.1 6.4 - - - +
502B PHE* 3.6 20.3 - - - +
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Residues in contact with TYR 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU 4.5 1.9 + - - -
211B LEU* 3.8 26.0 - - + +
212B GLU* 3.2 37.4 + - - +
215B TYR* 3.7 25.8 - + + -
436B LEU 3.0 17.7 + - - +
437B PRO* 3.7 5.6 - - + +
439B GLY* 1.3 79.4 - - - +
441B LEU* 1.3 62.2 + - - +
442B VAL 3.5 0.5 + - - -
443B ASP 4.0 1.4 + - - -
444B GLN* 3.0 46.8 + - + +
447B TRP* 5.8 2.2 - + - -
470B TYR* 3.6 26.1 + + - -
499B ILE* 4.1 17.1 - - + +
502B PHE* 3.8 19.5 - + + -
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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
----------------------------------------------------------
437B PRO 2.9 22.6 + - - +
438B PHE* 3.2 10.0 + - + +
440B TYR* 1.3 76.8 - - - +
442B VAL* 1.3 78.6 + - + +
444B GLN* 3.1 12.5 + - - +
445B TRP* 2.9 20.4 + - - +
463B TRP* 4.0 20.6 - - + -
466B LEU* 3.9 32.4 - - + +
467B ARG* 4.0 15.3 - - + -
470B TYR* 3.9 23.3 - - + -
471B GLN* 3.6 23.8 - - + +
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B PHE* 3.3 50.7 + - + +
439B GLY 4.5 0.2 + - - -
440B TYR 3.5 1.0 - - - -
441B LEU* 1.3 85.9 - - + +
443B ASP* 1.3 63.7 + - - +
445B TRP* 3.2 7.6 + - + +
446B ARG* 3.0 29.5 + - - +
463B TRP* 4.2 11.4 - - + -
489B LYS* 5.4 4.0 - - + -
491B HIS* 5.7 0.9 - - + -
492B VAL* 4.6 16.8 - - + -
498B TYR* 3.7 34.3 - - + -
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Residues in contact with ASP 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B TRP* 4.3 4.7 - - - -
439B GLY 5.0 1.0 + - - -
440B TYR 4.0 3.9 + - - +
442B VAL* 1.3 75.8 - - - +
444B GLN* 1.3 59.0 + - - +
445B TRP 3.2 0.7 - - - -
446B ARG* 2.7 39.4 + - - +
447B TRP* 2.7 67.2 + - + +
497B PRO* 3.9 6.8 - - - +
498B TYR* 2.9 26.3 + - - +
499B ILE* 3.0 25.0 + - + +
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Residues in contact with GLN 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B TYR* 3.0 49.2 + - + +
441B LEU* 3.1 12.3 + - - +
443B ASP* 1.3 77.2 - - - +
445B TRP* 1.3 61.8 + - - +
447B TRP* 4.1 18.5 - - + +
448B GLY* 3.2 17.7 + - - -
453B ARG* 4.3 8.3 + - - -
466B LEU* 4.1 16.3 - - + +
469B LYS* 5.2 1.9 + - - -
470B TYR* 3.0 42.4 + - - -
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Residues in contact with TRP 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 4.2 16.4 - + - -
441B LEU 2.9 9.1 + - - +
442B VAL 3.3 11.7 - - - +
444B GLN* 1.3 76.9 - - - +
446B ARG* 1.3 77.3 + - + +
448B GLY* 3.2 4.0 + - - -
449B VAL* 3.1 52.7 + - + +
454B THR* 4.3 5.9 + - + +
459B TYR* 3.0 33.1 + + - +
462B ASP* 3.9 10.9 - - + -
463B TRP* 3.5 40.1 - + + +
466B LEU* 3.5 15.6 - - + +
484B PHE* 3.6 32.5 - + - -
486B ALA* 3.7 21.5 - - + -
492B VAL* 4.2 18.8 - - + -
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Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 3.3 23.5 + - - +
178B PHE* 6.2 0.2 - - - -
198B TRP* 3.5 22.5 - - + -
442B VAL* 3.0 19.8 + - - +
443B ASP* 2.7 28.3 + - - +
445B TRP* 1.3 87.7 - - + +
447B TRP* 1.3 61.7 + - + +
449B VAL* 3.2 5.2 + - + +
450B PHE* 2.9 50.9 + - + -
491B HIS* 2.9 32.5 + - - +
492B VAL* 3.7 14.9 + - - +
495B VAL* 4.2 1.8 - - - +
496B THR 2.8 27.8 + - - +
497B PRO* 3.5 0.6 - - - +
498B TYR* 3.4 16.6 - - - +
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Residues in contact with TRP 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASP* 4.9 1.4 - - - +
195B GLY* 4.0 14.9 + - - -
198B TRP* 4.7 12.3 - + - +
199B ARG* 3.3 52.8 + - + +
207B PHE* 4.2 1.6 - + - -
208B GLU* 3.8 31.6 - - + -
211B LEU* 3.9 26.7 - - + -
440B TYR* 5.8 2.0 - + - -
443B ASP* 2.7 53.9 + - + +
444B GLN* 4.1 17.9 - - + +
446B ARG* 1.3 73.8 - - - +
448B GLY* 1.3 57.9 + - - +
450B PHE* 3.8 6.0 - + - +
451B SER* 3.0 30.0 + - - -
453B ARG* 6.1 0.4 - - - +
499B ILE* 4.1 23.5 - - + +
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Residues in contact with GLY 448 (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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444B GLN 3.2 6.6 + - - -
445B TRP 3.2 7.0 + - - -
446B ARG 3.2 0.8 - - - -
447B TRP* 1.3 75.9 - - - +
449B VAL* 1.3 63.0 + - - +
451B SER* 3.1 9.5 + - - -
453B ARG* 3.0 37.5 + - - +
454B THR* 3.0 28.8 + - - -
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Residues in contact with VAL 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 4.3 8.3 - - + +
179B THR* 3.9 31.6 - - + +
183B ASN* 4.8 0.2 + - - -
445B TRP* 3.1 45.4 + - + +
446B ARG* 3.7 9.2 - - + +
448B GLY* 1.3 75.0 - - - +
450B PHE* 1.3 65.5 + - + +
452B GLY* 3.1 13.5 + - - -
454B THR* 3.5 26.9 - - + +
459B TYR* 3.8 22.7 - - + +
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Residues in contact with PHE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 4.6 1.6 - - - -
178B PHE* 4.1 25.1 - + - -
179B THR* 4.0 16.8 - - + -
182B SER* 4.0 9.0 - - - -
183B ASN* 2.8 40.5 + - - +
187B LYS* 5.4 0.3 + - - -
193B ASP* 3.4 24.6 - - - +
194B THR* 3.5 25.4 - - + -
195B GLY* 3.7 18.2 - - - +
198B TRP* 3.7 28.7 - + - -
446B ARG* 2.9 46.1 + - + +
447B TRP* 3.8 3.6 - + - +
449B VAL* 1.3 79.2 - - + +
451B SER* 1.3 59.1 + - - +
452B GLY 3.4 0.7 + - - -
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Residues in contact with SER 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASP* 3.4 19.9 + - - -
447B TRP 3.0 15.5 + - - -
448B GLY* 3.1 14.4 + - - -
450B PHE* 1.3 75.8 - - - +
452B GLY* 1.3 57.4 + - - +
453B ARG* 3.2 18.1 + - - +
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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