Contacts of the helix formed by residues 434 - 442 (chain B) in PDB entry 3K5N
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 434 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TYR* 1.8 37.1 + - - -
432B LEU 3.5 5.4 + - - +
433B ILE* 1.3 80.5 - - - +
435B PRO* 1.4 70.6 - - - +
436B VAL* 2.3 25.8 - - - +
437B GLY* 2.8 8.5 + - - +
438B LEU* 2.8 28.8 + - - +
459B PHE* 3.5 3.7 - - - -
464B HIS* 3.2 9.8 - - + +
465B CYS 3.2 16.7 + - - +
466B LEU* 3.9 2.5 - - + -
467B PRO* 3.7 16.8 - - + -
515B LEU* 4.0 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 4.1 9.8 - - + -
373B PHE* 4.4 11.4 - - + -
377B TYR* 3.4 19.1 - - + +
433B ILE 4.8 0.2 - - - +
434B ASP* 1.4 88.7 - - - +
436B VAL* 1.3 64.1 + - - +
437B GLY 3.1 1.3 - - - -
438B LEU* 3.2 8.6 + - + +
439B VAL* 3.1 24.3 + - - +
466B LEU* 5.0 3.8 - - + -
503B LEU* 4.6 5.2 - - + -
510B PHE* 4.2 29.6 - - + +
515B LEU* 3.7 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 4.2 14.3 - - + -
377B TYR* 2.9 10.7 + - + +
381B MET* 5.4 2.2 - - + +
384B ALA* 4.4 13.5 - - + -
386B TYR* 3.5 35.4 - - + -
434B ASP* 2.3 40.8 - - - +
435B PRO* 1.3 76.8 - - - +
437B GLY* 1.3 54.1 + - - +
439B VAL* 3.1 6.0 + - - +
440B GLU* 2.7 35.9 + - + +
463B LYS* 4.3 9.4 - - + +
465B CYS* 3.4 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B LEU 5.7 0.9 - - - -
434B ASP* 2.8 17.9 + - - -
435B PRO 3.1 0.4 - - - -
436B VAL* 1.3 86.3 - - - +
438B LEU* 1.3 50.5 + - - +
440B GLU* 4.1 0.2 - - - -
441B GLY 2.7 27.2 + - - -
459B PHE* 4.3 3.4 - - - -
460B SER* 3.0 23.5 + - - -
463B LYS 3.3 17.5 - - - -
464B HIS* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ASP 2.8 17.0 + - - +
435B PRO* 3.6 8.7 - - + +
436B VAL 3.2 0.4 - - - -
437B GLY* 1.3 74.5 - - - +
439B VAL* 1.3 66.8 + - + +
442B MET* 3.0 30.5 + - + +
457B ALA* 3.8 19.3 - - + -
458B TRP 3.8 9.2 - - - +
459B PHE* 3.5 30.0 - - + -
512B ASP* 3.2 33.9 - - + +
514B ARG* 3.5 27.4 - - + +
515B LEU* 5.0 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 3.4 45.8 - - + +
75B ARG* 4.2 12.1 - - - -
386B TYR* 3.8 31.2 - - + +
435B PRO 3.1 9.6 + - - +
436B VAL* 3.1 10.5 + - - +
438B LEU* 1.3 78.9 - - + +
440B GLU* 1.3 66.6 - - - +
441B GLY 3.4 0.3 + - - -
442B MET* 3.5 12.5 + - - +
443B ALA* 3.5 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 5.5 0.5 - - - -
75B ARG* 4.7 5.8 + - - +
386B TYR* 2.7 30.8 + - - +
436B VAL* 2.7 18.7 + - + +
437B GLY 3.7 3.8 - - - +
439B VAL* 1.3 78.9 - - - +
441B GLY* 1.3 55.9 + - - +
443B ALA* 2.4 30.5 - - - +
444B GLN* 3.6 15.7 + - - +
460B SER* 3.5 10.5 - - - +
463B LYS* 2.3 62.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B GLY 2.7 20.0 + - - -
439B VAL 3.1 0.4 - - - -
440B GLU* 1.3 73.3 - - - +
442B MET* 1.3 61.5 + - - +
443B ALA 2.8 6.1 - - - -
444B GLN* 2.9 29.5 + - - +
445B PRO 3.5 1.0 - - - -
450B SER* 4.3 3.1 - - - -
458B TRP* 3.5 17.4 - - - +
459B PHE 4.2 0.7 - - - -
460B SER* 3.7 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU* 3.0 14.6 + - + +
439B VAL* 3.5 6.3 + - - +
440B GLU 3.5 0.4 - - - -
441B GLY* 1.3 73.6 - - - +
443B ALA* 1.3 60.8 + - - +
444B GLN 3.3 0.4 - - - -
445B PRO* 4.0 16.5 - - + +
456B ASP* 3.9 12.1 - - - +
457B ALA* 4.3 1.1 - - - -
458B TRP* 2.7 58.8 - - + +
514B ARG* 3.9 27.4 - - - +
----------------------------------------------------------
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