Contacts of the helix formed by residues 354 - 364 (chain A) 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 TRP 354 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 6.3 0.6 - - - +
27A VAL* 3.2 44.5 + - + +
28A VAL 4.2 0.2 - - - -
29A ALA* 3.7 25.4 - - + -
43A VAL* 3.5 16.6 - - + -
44A HIS* 3.6 28.2 + + - -
60A VAL* 4.8 1.2 - - + +
66A ILE* 3.6 15.7 - - + -
69A VAL* 3.8 27.8 - - + -
95A ILE* 3.4 29.8 - - + -
96A ARG* 4.5 1.3 - - - -
97A ASP* 4.3 16.0 + - + +
352A ASN* 3.1 23.2 + - - +
353A PRO* 1.3 85.3 - - + +
355A PHE* 1.3 63.0 + - - +
356A GLN 3.4 1.6 - - - -
357A GLU* 3.2 17.9 + - - +
358A PHE* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 3.8 21.8 - - + -
70A GLU* 4.1 0.4 - - - -
341A TYR* 4.8 2.0 - + - -
344A LEU* 3.9 26.0 - - + -
345A ARG 4.0 5.6 - - - -
346A PRO* 3.9 28.5 - - + -
349A ASN* 3.3 33.0 - - + +
352A ASN* 3.2 26.1 + - - +
353A PRO 3.3 0.4 - - - -
354A TRP* 1.3 77.9 - - - +
356A GLN* 1.3 52.9 + - + +
358A PHE* 3.2 23.8 + + - +
359A TRP* 2.7 68.0 + + - +
387A LEU* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PRO* 3.3 28.7 + - + +
347A GLU* 4.9 1.8 - - - +
349A ASN 5.6 2.2 - - - +
350A HIS* 3.7 25.2 - - - +
352A ASN 4.8 0.6 + - - +
353A PRO 4.6 5.9 + - - +
354A TRP 3.4 0.8 - - - -
355A PHE* 1.3 74.7 - - + +
357A GLU* 1.3 65.9 + - - +
359A TRP* 3.7 2.2 - - - +
360A GLN* 3.0 32.9 + - - +
367A LEU* 4.0 23.6 - - + +
369A GLY 4.6 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A HIS* 2.8 40.3 + - - -
58A GLY 5.0 0.5 - - - +
59A ALA* 5.4 0.7 - - - -
60A VAL* 3.9 17.7 + - + +
353A PRO 5.1 1.7 + - - +
354A TRP* 3.2 19.6 + - - +
356A GLN* 1.3 76.8 - - - +
358A PHE* 1.3 59.3 + - - +
360A GLN* 3.3 6.5 + - - +
361A HIS* 2.9 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 3.8 19.9 - - + +
61A ARG 5.0 0.2 - - - -
62A GLU* 3.6 39.0 - - + -
66A ILE* 3.6 38.1 - - + -
341A TYR* 3.5 24.9 - - - -
354A TRP 2.9 10.5 + - - +
355A PHE* 3.2 30.0 + + - +
357A GLU* 1.3 74.9 - - - +
359A TRP* 1.3 67.3 + + - +
361A HIS* 3.2 2.1 + - - +
362A ARG* 2.8 46.9 + - + +
387A LEU* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU 4.1 4.5 - - - -
345A ARG* 3.6 23.6 - - - -
346A PRO* 3.6 40.4 - - + +
355A PHE* 2.7 42.2 + + - +
356A GLN* 3.7 4.3 - - - +
358A PHE* 1.3 77.9 - + - +
360A GLN* 1.3 62.6 + - - +
362A ARG* 4.6 1.3 - - - -
363A PHE* 3.2 60.7 + + - +
367A LEU* 3.9 18.3 - - + +
381A CYS* 4.3 9.2 - - - +
382A ASN 5.5 0.8 + - - -
385A LEU* 3.7 32.1 - - + +
386A THR* 4.2 3.1 - - - -
387A LEU* 3.6 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLN* 3.0 22.1 + - - +
357A GLU* 3.7 6.1 - - - +
359A TRP* 1.3 78.0 - - - +
361A HIS* 1.3 57.5 + - - +
364A GLN* 3.0 23.6 + - - +
365A CYS* 3.3 30.3 + - - +
366A ARG* 3.9 7.9 - - - -
367A LEU* 3.7 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA* 4.3 19.6 - - + +
60A VAL* 3.8 34.9 + - + +
357A GLU* 2.9 18.1 + - + +
358A PHE* 3.8 1.2 - - - +
360A GLN* 1.3 76.5 - - - +
362A ARG* 1.3 68.5 + - - +
363A PHE 3.2 0.7 + - - -
364A GLN* 3.4 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 2.8 45.9 + - - -
358A PHE* 2.8 41.5 + - + +
359A TRP 3.9 2.0 - - - +
361A HIS* 1.3 77.3 + - - +
363A PHE* 1.3 93.2 + - + +
364A GLN* 3.6 2.0 - - - +
386A THR 4.7 0.2 + - - -
387A LEU* 3.8 20.5 + - + +
389A THR 2.6 31.3 + - - -
390A HIS* 4.1 23.6 + - - +
391A HIS* 5.3 2.4 + - - +
392A VAL 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A TRP* 3.2 65.5 + + - +
361A HIS 3.2 0.2 - - - -
362A ARG* 1.3 112.3 - - + +
364A GLN* 1.3 72.2 + - - +
365A CYS* 3.2 20.0 + - - +
385A LEU* 3.9 26.4 - - + +
386A THR 3.6 32.3 - - - -
387A LEU* 4.3 4.9 - - + -
389A THR* 5.7 2.9 - - - -
390A HIS* 6.3 2.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLN 3.0 13.1 + - - +
361A HIS* 3.4 23.5 + - - +
362A ARG 5.2 1.1 - - - +
363A PHE* 1.3 79.7 - - - +
365A CYS* 1.3 56.5 + - - +
378A ASN 5.3 3.4 + - - -
379A LYS* 5.0 8.0 + - - +
----------------------------------------------------------
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