Contacts of the helix formed by residues 433 - 443 (chain B) in PDB entry 3LMK
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 433 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B MET* 3.8 8.4 - - + +
418B LEU* 6.4 0.2 - - + -
428B ALA 5.5 0.8 + - - -
431B PRO 3.4 4.7 + - - +
432B ILE* 1.3 73.6 - - - +
434B GLY* 1.3 65.1 - - - +
435B ARG* 2.9 24.1 + - - +
436B LYS* 2.9 39.9 + - + +
437B LEU* 3.0 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL 5.5 1.3 - - - -
166B ASN* 3.0 29.6 - - - +
168B PRO* 3.8 4.6 - - - +
187B TYR* 3.7 4.0 - - - -
432B ILE* 3.5 7.7 + - - -
433B ASP* 1.3 71.4 + - - +
435B ARG* 1.3 55.4 + - - +
437B LEU* 3.2 10.7 + - - +
438B LEU* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASN* 4.2 9.3 + - - +
186B LYS* 4.8 15.0 - - - +
187B TYR* 3.5 24.0 + - - +
433B ASP* 2.9 14.8 + - - +
434B GLY* 1.3 77.1 - - - +
436B LYS* 1.3 66.3 + - + +
438B LEU* 3.6 5.0 + - + +
439B GLU* 3.2 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B MET* 3.8 19.3 - - + +
418B LEU* 4.8 15.5 - - + -
433B ASP* 2.9 24.8 + - + +
435B ARG* 1.3 81.1 - - - +
437B LEU* 1.3 65.7 + - - +
439B GLU* 3.2 29.5 + - - +
440B SER* 3.0 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL* 3.4 44.9 - - + +
168B PRO* 3.9 12.3 - - + -
407B MET* 4.4 10.8 - - - +
410B GLY 3.9 24.9 - - - +
411B LEU* 3.9 22.9 - - + +
414B MET* 3.9 15.5 - - - -
432B ILE* 4.5 4.0 - - + -
433B ASP 3.0 10.9 + - - +
434B GLY* 3.2 10.3 + - - +
436B LYS* 1.3 77.2 - - - +
438B LEU* 1.3 51.8 + - - +
440B SER* 3.1 5.7 + - - -
441B LEU* 2.7 44.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
168B PRO* 3.8 6.4 - - + +
186B LYS* 3.5 49.6 - - + +
187B TYR* 3.8 34.3 - - + +
189B MET* 3.6 32.8 - - + -
434B GLY 2.9 17.2 + - - +
435B ARG* 3.7 6.7 - - + +
437B LEU* 1.3 77.1 - - - +
439B GLU* 1.3 56.3 + - + +
441B LEU* 4.3 2.7 - - - -
442B MET* 2.8 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ARG* 3.2 25.4 + - + +
436B LYS* 3.2 36.6 + - - +
438B LEU* 1.3 75.4 - - + +
440B SER* 1.3 62.7 + - - +
442B MET* 3.5 6.1 + - - +
443B LYS* 3.5 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B GLY* 2.6 32.6 + - - -
413B ASN* 3.7 13.7 + - - +
414B MET* 3.4 19.4 + - - -
436B LYS 3.0 12.4 + - - -
437B LEU* 3.3 11.0 - - - -
439B GLU* 1.3 77.1 - - - +
441B LEU* 1.3 61.1 + - - +
443B LYS* 3.2 26.9 + - - +
444B THR* 4.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PRO* 3.4 37.2 - - + -
170B ILE* 3.8 21.3 - - + -
189B MET* 3.7 20.6 - - + -
406B SER 3.3 27.8 - - - +
407B MET* 3.9 11.4 - - - +
410B GLY* 3.6 11.9 - - - -
437B LEU* 2.7 29.8 + - + +
438B LEU 3.8 2.7 - - - +
440B SER* 1.3 69.8 - - - +
442B MET* 1.3 61.1 + - - +
443B LYS 3.0 4.9 + - - -
444B THR* 2.4 30.2 + - - +
456B PHE* 3.2 10.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
182B LYS* 4.8 12.8 - - + -
186B LYS 5.4 0.9 - - - +
189B MET* 3.8 25.8 - - - +
438B LEU* 2.8 41.4 + - + +
439B GLU* 3.9 7.4 - - - +
440B SER 3.4 0.2 - - - -
441B LEU* 1.3 72.0 - - - +
443B LYS* 1.3 60.7 + - + +
444B THR 3.4 3.0 + - - -
456B PHE* 4.1 19.9 - - - +
457B ASP 3.9 8.7 - - - +
458B GLU* 3.5 35.0 - - - +
459B ASN 4.6 0.9 - - - -
460B GLY* 4.0 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASN* 5.0 7.4 + - - -
439B GLU* 3.5 25.8 + - - +
440B SER* 3.2 16.2 + - - +
441B LEU 3.0 1.6 - - - -
442B MET* 1.3 78.7 - - + +
444B THR* 1.3 61.1 + - - +
445B ASN* 3.4 8.2 + - - +
----------------------------------------------------------
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