Contacts of the helix formed by residues 485 - 498 (chain B) in PDB entry 2H5G
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 ASP 485 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B SO4 5.6 2.3 + - - -
425B ARG 4.4 5.1 - - - +
427B SER 5.5 3.6 - - - -
428B LEU* 3.6 23.3 - - + +
432B LYS* 4.0 21.6 - - + +
436B LEU* 3.8 11.4 - - + +
483B ARG* 3.5 20.4 - - - +
484B PRO* 1.3 77.8 - - - +
486B CYS* 1.3 63.9 + - - +
487B LEU 3.3 0.2 - - - -
488B PRO* 3.5 10.1 - - - +
489B GLN* 3.3 27.1 + - - +
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Residues in contact with CYS 486 (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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478B VAL* 4.8 3.4 - - - -
480B PHE* 3.6 35.7 - - - -
483B ARG* 3.0 22.7 + - + +
485B ASP* 1.3 80.2 + - - +
487B LEU* 1.3 69.4 + - - +
488B PRO 3.4 0.2 - - - -
489B GLN* 3.1 14.7 + - + +
490B VAL* 2.9 33.9 + - + +
558B ARG* 3.9 31.0 - - - +
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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
----------------------------------------------------------
480B PHE* 4.2 12.6 - - + -
484B PRO 3.1 9.2 + - - +
486B CYS* 1.3 82.2 - - - +
488B PRO* 1.4 67.3 - - + +
490B VAL* 3.3 8.1 + - - +
491B ALA* 3.0 33.0 + - + +
503B LEU* 3.8 33.9 - - + -
513B ASN* 3.6 46.4 - - + +
516B LEU* 3.9 17.3 - - + +
517B HIS* 4.0 5.2 - - + +
520B THR* 3.8 21.3 - - - +
535B LEU* 4.6 2.7 - - + -
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Residues in contact with PRO 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 4.5 8.8 - - + +
396B LEU* 4.3 23.8 - - + -
436B LEU* 4.1 17.9 - - + -
440B LEU* 3.9 13.0 - - + +
484B PRO 3.4 13.5 - - - +
485B ASP 3.5 10.8 - - - +
487B LEU* 1.4 98.0 - - + +
489B GLN* 1.3 60.9 + - - +
491B ALA* 4.1 5.1 - - + +
492B ALA* 3.0 26.5 + - - +
516B LEU* 4.0 23.3 - - + -
520B THR* 5.1 1.1 - - - +
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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
----------------------------------------------------------
436B LEU* 3.6 27.2 - - + +
440B LEU* 4.6 4.3 - - + -
485B ASP* 3.3 28.3 + - - +
486B CYS* 3.1 14.3 + - - +
488B PRO* 1.3 78.9 - - - +
490B VAL* 1.3 62.5 + - - +
492B ALA* 3.5 1.6 + - - +
493B LEU* 3.1 30.7 + - - +
558B ARG* 6.0 1.2 - - - +
729B ASP* 5.2 3.3 - - - +
731B TYR* 5.3 5.4 + - - +
736B GLY 5.5 0.9 - - - +
737B ALA* 3.5 23.2 - - + +
738B GLU* 3.4 37.2 + - - +
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Residues in contact with VAL 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B LEU* 5.6 0.5 - - - +
478B VAL* 4.1 27.4 - - + -
486B CYS* 2.9 20.9 + - + +
487B LEU* 3.4 11.7 - - - +
489B GLN* 1.3 72.9 - - - +
491B ALA* 1.3 63.7 + - - +
493B LEU* 3.9 0.7 - - - +
494B ALA* 2.9 30.3 + - - +
501B LEU* 3.9 6.2 - - + +
503B LEU* 3.6 28.0 - - + -
558B ARG* 4.6 5.2 - - - +
738B GLU 4.2 2.9 - - - +
739B VAL* 3.9 43.4 - - + +
757B LEU* 5.3 0.2 - - - +
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Residues in contact with ALA 491 (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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392B LEU* 4.8 2.0 - - + -
487B LEU* 3.0 22.3 + - + +
488B PRO* 4.1 3.6 - - + +
490B VAL* 1.3 79.0 - - - +
492B ALA* 1.3 56.5 + - - +
494B ALA* 3.2 2.8 + - - +
495B ILE* 2.9 37.4 + - + +
501B LEU* 3.7 17.9 - - + -
520B THR* 3.8 33.7 - - + +
533B VAL* 4.7 3.8 - - + -
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Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ILE* 3.5 17.2 - - + +
392B LEU* 4.9 3.1 - - + +
440B LEU* 3.6 29.2 - - + -
443B ILE* 4.1 11.4 - - + -
488B PRO 3.0 20.1 + - - +
489B GLN 4.0 2.2 - - - +
491B ALA* 1.3 76.4 - - - +
493B LEU* 1.3 58.0 + - - +
495B ILE* 3.4 10.2 + - - +
496B ALA* 2.9 30.2 + - - +
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ILE* 3.9 28.3 - - + -
489B GLN 3.1 19.3 + - - +
490B VAL 4.0 2.9 - - - +
492B ALA* 1.3 73.5 - - - +
494B ALA* 1.3 57.0 + - - +
496B ALA* 3.5 3.7 + - - +
497B SER* 2.6 33.9 + - - -
735B LEU 4.6 2.9 - - - +
737B ALA* 3.8 4.9 - - + +
738B GLU* 3.4 44.6 - - - +
739B VAL* 3.6 11.9 - - + +
752B VAL 4.1 4.0 - - - +
753B GLY* 4.1 4.5 - - - -
754B LEU* 3.5 31.1 - - + +
757B LEU* 3.7 15.6 - - + +
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Residues in contact with ALA 494 (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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476B LEU* 4.2 14.6 - - + -
490B VAL 2.9 19.4 + - - +
491B ALA 3.2 4.0 + - - +
493B LEU* 1.3 73.6 - - - +
495B ILE* 1.3 65.3 + - + +
497B SER* 3.1 6.8 + - - -
498B GLY 3.0 4.3 + - - -
499B ASN* 2.9 41.6 + - - +
501B LEU* 4.1 22.9 - - + -
533B VAL* 5.6 1.3 - - + -
757B LEU* 4.0 4.0 - - - +
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Residues in contact with ILE 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 3.8 23.7 - - + +
385B ARG* 3.1 36.9 - - + +
388B ILE* 4.0 20.6 - - + -
389B ILE* 3.7 20.2 - - + -
392B LEU* 5.0 6.7 - - + -
491B ALA* 2.9 27.4 + - + +
492B ALA* 3.7 7.9 - - - +
494B ALA* 1.3 76.7 - - + +
496B ALA* 1.3 62.5 + - - +
498B GLY* 3.2 6.4 + - - -
520B THR* 4.3 14.4 - - + +
523B ALA* 6.1 0.2 - - + -
524B LEU* 3.8 30.1 - - + -
533B VAL* 4.7 7.4 - - + -
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Residues in contact with ALA 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B ARG* 4.1 9.8 + - - +
389B ILE* 3.6 10.3 - - + +
443B ILE* 3.6 23.8 - - + -
447B SER* 3.9 13.5 + - - +
450B SER* 4.3 4.0 - - - -
451B VAL* 3.6 15.1 - - - +
492B ALA 2.9 18.3 + - - +
493B LEU 3.9 3.8 - - - +
495B ILE* 1.3 76.7 - - - +
497B SER* 1.3 57.0 + - - +
498B GLY 3.4 0.2 - - - -
754B LEU* 3.8 23.4 - - + +
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Residues in contact with SER 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B VAL* 3.7 11.2 - - - +
472B PRO* 3.4 19.1 - - - +
493B LEU 2.6 23.1 + - - -
494B ALA* 3.1 5.0 + - - -
496B ALA* 1.3 75.9 - - - +
498B GLY* 1.3 63.1 + - - +
499B ASN* 2.8 24.3 + - - -
754B LEU* 4.0 17.3 - - - -
757B LEU* 3.5 15.5 - - - +
758B LEU* 3.6 17.1 - - - +
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Residues in contact with GLY 498 (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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374B GLY 3.2 21.6 - - - +
377B LEU* 4.5 5.4 - - - -
378B ALA* 3.9 19.1 - - - +
385B ARG* 4.4 3.3 - - - +
451B VAL* 4.3 2.6 - - - +
472B PRO* 3.2 21.4 - - - +
474B GLY 4.7 0.7 - - - +
494B ALA 3.0 3.4 + - - -
495B ILE 3.2 11.2 + - - -
496B ALA 3.4 1.0 + - - -
497B SER* 1.3 78.8 - - - +
499B ASN* 1.3 59.9 + - - +
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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
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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