Contacts of the helix formed by residues 482 - 495 (chain B) in PDB entry 3H8E
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 ARG 482 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B MET* 5.2 0.7 - - + -
387B SER 3.6 6.5 + - - -
388B HIS* 2.6 40.2 + - - +
390B THR* 4.6 1.2 + - - +
411B ASP 5.1 0.8 + - - -
412B ASP* 2.0 66.8 + - - +
413B ARG 3.2 27.3 + - - +
468B THR* 2.8 45.2 - - - +
480B THR* 3.0 28.0 + - + +
481B GLY* 1.3 74.2 - - - +
483B PRO* 1.3 69.4 - - + +
485B PRO* 4.1 2.0 - - - -
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Residues in contact with PRO 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B THR* 5.4 3.1 - - + -
292B CYS* 4.3 1.6 - - + +
296B SER* 2.7 42.6 - - - +
374B ILE* 4.4 5.8 - - + -
390B THR* 5.8 0.4 - - - +
412B ASP* 3.6 0.7 - - - +
463B MET* 5.3 6.0 - - + +
465B ILE* 3.6 37.0 - - + -
469B ALA* 4.7 4.0 - - + -
480B THR* 4.7 3.4 - - - +
481B GLY 3.4 1.1 - - - -
482B ARG* 1.3 96.4 - - + +
484B VAL* 1.3 62.3 + - - -
485B PRO 3.4 0.3 - - - -
486B LEU* 3.4 3.5 + - - +
487B LEU* 3.1 34.6 + - + +
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Residues in contact with VAL 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 3.8 26.2 - - + +
182B GLY* 4.5 0.4 - - - -
183B MET* 3.7 15.3 - - + +
186B THR* 3.4 30.1 - - + +
296B SER* 4.0 14.8 - - - +
299B GLY 4.2 13.5 - - - +
300B THR* 3.9 8.5 - - - +
303B ALA* 4.9 0.4 - - + -
481B GLY 3.1 14.4 + - - +
483B PRO* 1.3 77.5 - - - +
485B PRO* 1.3 64.3 - - + +
488B THR* 2.7 42.4 + - - +
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Residues in contact with PRO 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLU* 3.0 29.6 - - - +
179B ILE* 3.8 16.0 - - + +
183B MET* 3.7 11.7 - - + -
410B ALA* 3.7 16.5 - - + +
412B ASP* 3.2 27.1 - - + +
481B GLY 2.9 25.1 - - - +
482B ARG* 3.3 2.5 - - - +
484B VAL* 1.3 80.3 - - + +
486B LEU* 1.3 56.9 + - - +
488B THR* 3.8 0.7 - - - -
489B GLN* 2.8 31.9 + - - +
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Residues in contact with LEU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B THR* 5.6 1.1 - - - -
403B LEU* 3.7 47.1 - - + +
406B ALA* 3.7 2.7 - - + +
407B GLY* 3.7 15.7 - - - +
410B ALA* 4.3 9.4 - - - -
412B ASP* 2.9 40.5 + - - +
413B ARG 4.7 0.2 - - - -
414B ALA* 4.0 21.5 - - + -
463B MET* 4.0 23.6 - - + -
482B ARG 4.9 0.2 - - - +
483B PRO 3.4 3.8 + - - +
485B PRO* 1.3 75.4 - - - +
487B LEU* 1.4 62.4 + - + +
489B GLN* 3.2 3.8 + - - +
490B TYR* 2.8 25.6 + - - +
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 4.2 18.8 - - + -
296B SER* 4.3 6.7 - - - +
297B VAL 5.2 0.2 - - - +
300B THR* 3.5 31.2 - - + +
372B ILE* 4.3 11.4 - - + -
374B ILE* 4.0 28.0 - - + -
403B LEU* 4.7 0.9 - - + -
463B MET* 3.8 27.6 - - + -
483B PRO* 3.1 30.4 + - + +
486B LEU* 1.4 86.4 - - + +
488B THR* 1.3 62.0 + - - +
490B TYR* 3.2 6.9 + - + +
491B LEU* 3.0 27.3 + - + +
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Residues in contact with THR 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 3.7 26.5 - - + -
300B THR* 3.9 12.0 - - - +
303B ALA* 3.8 23.4 - - + +
304B VAL* 5.2 5.8 - - + +
307B LEU* 4.3 18.2 - - + -
309B LEU* 5.0 1.1 - - + +
484B VAL* 2.7 35.9 + - - +
485B PRO 3.9 0.4 - - - -
487B LEU* 1.3 75.2 - - - +
489B GLN* 1.3 58.6 + - - +
491B LEU* 3.1 5.3 + - - +
492B LEU* 2.8 32.6 + - + +
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Residues in contact with GLN 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B TYR* 5.1 1.6 + - - -
128B ARG* 2.8 47.4 + - - +
179B ILE* 5.2 0.6 - - - +
406B ALA* 3.4 28.7 - - - +
409B ARG* 3.3 21.6 + - - +
410B ALA* 3.9 14.4 - - + +
485B PRO 2.8 19.0 + - - +
486B LEU 3.5 4.7 - - - +
488B THR* 1.3 77.1 - - - +
490B TYR* 1.4 56.4 + - - +
492B LEU* 3.3 15.5 + - - +
493B ASP* 2.9 52.9 + - - +
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Residues in contact with TYR 490 (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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262B PHE* 3.3 17.1 - + + -
264B LEU* 5.8 0.9 - - + -
370B ALA* 3.3 27.4 - - - +
372B ILE* 3.7 21.1 - - + -
399B LEU* 3.4 18.1 - - + +
402B GLN* 3.6 25.0 + - + -
403B LEU* 3.7 19.3 - - + -
406B ALA* 3.6 14.0 - - + +
486B LEU 2.8 19.8 + - - +
487B LEU* 3.5 7.0 - - + +
489B GLN* 1.4 70.9 - - - +
491B LEU* 1.3 81.3 + - + +
493B ASP* 3.2 6.9 + - - +
494B ARG* 2.9 64.2 + - + +
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Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 3.9 39.5 - - + -
264B LEU* 4.5 6.7 - - + -
300B THR* 3.8 19.7 - - + -
304B VAL* 3.7 25.6 - - + -
309B LEU* 3.8 16.1 - - + +
311B VAL* 4.6 9.6 - - + +
313B LEU* 4.0 20.0 - - + -
487B LEU 3.0 14.8 + - - +
488B THR 3.8 3.4 - - - +
490B TYR* 1.3 90.7 - - + +
492B LEU* 1.3 57.6 - - - +
494B ARG* 3.8 3.3 - - + +
495B ALA* 2.8 31.7 + - - +
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B TYR* 4.5 0.4 - - - +
128B ARG* 4.4 11.0 - - - +
175B HIS* 3.8 40.4 - - + +
179B ILE* 5.0 1.3 - - + -
307B LEU* 4.0 8.5 - - + -
309B LEU* 3.8 19.7 - - + +
488B THR* 2.8 32.5 + - + +
489B GLN* 3.5 26.7 - - - +
491B LEU* 1.3 73.8 - - - +
493B ASP* 1.3 61.8 + - - +
495B ALA 3.3 0.7 + - - -
496B GLY 3.0 3.8 + - - -
497B ALA* 2.9 55.5 + - + -
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Residues in contact with ASP 493 (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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402B GLN 4.6 1.6 - - - +
406B ALA* 3.8 13.5 + - - +
409B ARG* 2.7 44.9 + - - -
489B GLN* 2.9 30.3 + - - +
490B TYR* 3.2 8.7 + - - +
492B LEU* 1.3 77.4 - - - +
494B ARG* 1.3 87.6 + - - +
496B GLY* 3.2 12.5 + - - -
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Residues in contact with ARG 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 3.6 44.1 - - + -
311B VAL* 4.7 2.8 - - + +
369B GLN* 5.0 1.1 - - - +
402B GLN* 3.6 38.2 - - - +
490B TYR* 2.9 63.4 + - + +
491B LEU* 3.9 5.8 - - - +
493B ASP* 1.3 97.5 + - - +
495B ALA* 1.3 56.7 + - - +
496B GLY* 3.0 8.0 + - - -
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Residues in contact with ALA 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LEU* 4.2 14.4 - - + -
310B PRO* 3.9 32.4 - - + +
311B VAL* 3.7 21.5 - - + +
491B LEU 2.8 18.3 + - - +
492B LEU 4.0 2.9 - - - +
494B ARG* 1.3 75.1 - - - +
496B GLY* 1.3 64.8 + - - +
497B ALA* 3.3 3.2 + - + +
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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