Contacts of the helix formed by residues 429 - 447 (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 SER 429 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LEU* 4.3 4.3 - - - -
427B SER* 4.1 2.1 + - - -
428B LEU* 1.3 75.0 - - - +
430B THR* 1.3 66.6 + - - +
431B SER* 3.6 10.6 - - - -
432B LYS* 3.1 27.2 + - - +
433B LEU* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ARG* 3.4 30.5 - - - +
404B LEU* 4.3 14.1 - - - +
429B SER* 1.3 72.5 - - - +
431B SER* 1.3 61.2 + - - +
433B LEU* 3.7 6.2 + - - +
434B ASN* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B SER* 3.6 10.5 - - - -
430B THR* 1.3 81.7 - - - +
432B LYS* 1.3 66.2 + - - +
434B ASN* 3.1 9.9 + - - +
435B SER* 3.0 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B SER 5.7 1.1 - - - +
428B LEU* 4.4 6.3 - - + -
429B SER* 3.1 23.9 + - - +
431B SER* 1.3 78.1 - - - +
433B LEU* 1.3 58.1 + - - +
435B SER* 3.0 9.8 + - - +
436B LEU* 2.9 40.5 + - + +
485B ASP* 4.0 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 4.5 24.5 - - + +
397B THR* 5.4 0.6 + - - -
400B ARG* 3.8 25.6 - - + -
403B ILE* 3.8 43.5 - - + -
404B LEU* 3.8 23.6 - - + -
428B LEU* 4.6 13.7 - - + -
429B SER 3.0 15.4 + - - +
430B THR* 3.7 5.4 - - - +
432B LYS* 1.3 76.1 - - - +
434B ASN* 1.3 60.7 + - - +
436B LEU* 3.5 20.9 + - + +
437B ALA* 3.1 24.1 + - - +
516B LEU* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B THR* 5.9 0.7 - - - -
430B THR 3.1 15.8 + - - +
431B SER* 3.1 12.5 + - - +
433B LEU* 1.3 75.2 - - - +
435B SER* 1.3 62.8 + - - +
437B ALA* 3.4 7.2 + - - +
438B ILE* 3.0 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B SER* 3.0 15.3 + - - -
432B LYS* 3.5 11.3 - - - -
434B ASN* 1.3 78.3 + - - +
436B LEU* 1.3 56.2 + - - +
438B ILE* 3.2 11.2 + - - +
439B GLY* 2.7 32.2 + - - -
731B TYR* 3.8 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 3.8 13.7 - - + -
428B LEU* 4.7 1.6 - - + -
432B LYS* 2.9 35.4 + - + +
433B LEU* 3.6 23.6 - - + +
435B SER* 1.3 74.8 - - - +
437B ALA* 1.3 55.3 + - - +
439B GLY* 3.1 2.2 + - - +
440B LEU* 2.6 44.9 + - + +
485B ASP* 3.8 20.4 - - + +
488B PRO* 4.1 16.2 - - + -
489B GLN* 3.6 41.7 - - + +
516B LEU* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ALA* 3.6 31.2 - - - +
396B LEU* 4.1 7.8 - - + +
397B THR* 3.8 14.4 - - - +
433B LEU 3.1 15.0 + - - +
434B ASN* 3.7 7.0 - - - +
436B LEU* 1.3 77.3 - - - +
438B ILE* 1.3 63.6 + - - +
440B LEU 3.5 0.2 + - - -
441B ARG* 3.1 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ASN* 3.0 46.5 + - - +
435B SER* 3.7 7.2 - - - +
437B ALA* 1.3 74.1 - - + +
439B GLY* 1.3 64.1 + - - +
441B ARG* 3.3 19.2 + - - +
442B GLN* 3.1 31.0 + - + +
731B TYR* 3.8 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B SER 2.7 18.6 + - - -
436B LEU 3.5 2.9 - - - -
438B ILE* 1.3 71.7 - - - +
440B LEU* 1.3 64.1 + - - +
442B GLN* 3.1 18.0 + - - +
443B ILE* 3.1 20.0 + - - +
731B TYR* 4.0 2.7 - - - -
736B GLY* 3.1 31.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ILE* 3.2 14.5 - - + +
392B LEU* 3.7 39.0 - - + -
393B ALA* 3.7 21.1 - - + +
396B LEU* 3.9 17.9 - - + -
436B LEU* 2.6 28.5 + - + +
439B GLY* 1.3 73.6 - - - +
441B ARG* 1.3 56.5 + - - +
443B ILE* 3.3 11.5 + - + +
444B ALA* 2.9 24.6 + - - +
488B PRO* 3.9 25.1 - - + +
489B GLN* 4.6 6.3 - - + -
492B ALA* 3.6 17.5 - - + -
736B GLY 5.5 0.2 - - - +
737B ALA* 5.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B HIS* 4.0 27.0 + - + +
393B ALA* 3.8 15.0 + - + +
394B ASP* 3.8 23.2 + - - +
397B THR* 3.7 22.8 + - - +
434B ASN* 6.0 0.2 + - - -
437B ALA* 3.1 40.5 + - - +
438B ILE* 3.8 18.6 - - - +
439B GLY 3.3 0.4 - - - -
440B LEU* 1.3 77.2 - - - +
442B GLN* 1.3 57.8 + - - +
444B ALA* 3.4 7.8 + - - +
445B ALA* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ILE* 3.1 22.0 + - + +
439B GLY* 3.1 25.4 + - - +
441B ARG* 1.3 75.5 - - - +
443B ILE* 1.3 61.6 + - - +
445B ALA* 3.4 4.7 + - - +
446B SER* 2.9 30.7 + - - -
731B TYR* 3.5 17.8 + - - +
734B GLY* 4.7 17.6 + - - +
735B LEU 5.3 1.1 - - - -
736B GLY* 3.5 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ILE* 3.8 11.0 - - + -
439B GLY 3.1 17.0 + - - +
440B LEU* 3.3 15.5 + - + +
442B GLN* 1.3 72.9 - - - +
444B ALA* 1.3 66.6 + - - +
445B ALA 3.2 0.5 + - - -
446B SER* 3.2 9.2 + - - -
447B SER* 3.1 26.2 + - - -
492B ALA* 4.1 18.2 - - + +
493B LEU* 3.9 17.3 - - + -
496B ALA* 3.6 29.2 - - + -
735B LEU 3.8 17.9 - - - +
737B ALA* 3.8 27.8 - - + -
754B LEU* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ALA* 3.5 47.5 - - + +
389B ILE* 3.9 10.3 - - + +
390B HIS* 4.2 14.4 - - + +
440B LEU 2.9 17.4 + - - +
441B ARG* 3.7 8.3 - - - +
443B ILE* 1.3 78.2 - - - +
445B ALA* 1.3 61.5 + - - +
446B SER 3.4 0.3 + - - -
447B SER* 3.7 10.1 + - - -
448B GLN* 4.5 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ARG 2.9 18.8 + - - +
442B GLN* 3.4 5.1 + - - +
444B ALA* 1.3 76.5 - - - +
446B SER* 1.3 59.0 + - - +
447B SER 3.6 0.6 + - - -
448B GLN* 5.3 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B GLN 2.9 21.5 + - - -
443B ILE* 3.2 5.9 + - - -
445B ALA* 1.3 79.1 - - - +
447B SER* 1.3 60.6 + - - +
448B GLN 3.5 3.3 + - - -
449B ASP* 4.4 8.8 - - - +
450B SER* 4.4 2.4 + - - -
754B LEU* 5.3 3.9 - - - +
792B ARG* 5.6 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PRO* 5.0 2.6 + - - +
385B ARG* 5.5 5.0 + - - +
386B ALA* 4.9 6.4 + - - +
389B ILE* 4.8 2.4 - - - +
443B ILE 3.1 19.5 + - - -
444B ALA* 3.7 10.0 + - - -
445B ALA 3.6 1.2 - - - -
446B SER* 1.3 75.9 - - - +
448B GLN* 1.3 64.5 + - - +
449B ASP 3.4 2.7 - - - -
450B SER* 3.2 24.5 + - - -
451B VAL 4.9 0.2 + - - -
496B ALA* 3.9 20.5 + - - +
754B LEU* 3.5 24.7 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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