Contacts of the strand formed by residues 32 - 37 (chain M) in PDB entry 1LK3
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 MET 32 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M LEU* 3.8 29.6 - - + -
22M CYS* 3.8 11.4 - - - +
24M ALA* 4.2 5.6 - - + -
28M VAL* 4.1 10.3 - - + -
30M SER 2.9 6.4 + - - +
31M ARG* 1.3 73.1 - - - +
33M HIS* 1.3 66.1 + - - +
34M TRP* 4.3 11.3 - - + +
47M ILE 4.6 0.2 - - - +
48M TYR 4.0 0.2 - - - -
49M LYS 3.4 2.6 + - - -
50M ALA* 2.6 32.7 + - - +
70M PHE* 3.6 60.6 - - + -
87M CYS* 3.9 7.0 - - + -
88M GLN 3.4 29.8 - - - +
89M GLN* 4.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I TRP* 3.1 41.7 - + + +
31M ARG* 3.5 19.8 - - - -
32M MET* 1.3 72.3 - - - +
34M TRP* 1.3 68.3 + - - +
35M TYR* 4.6 1.3 - - + -
45M LEU* 4.3 5.4 - - + -
47M ILE 3.2 11.0 - - - +
48M TYR* 3.4 11.0 - - + -
49M LYS* 2.9 31.6 + - - -
87M CYS* 3.1 6.1 - - - +
88M GLN* 2.7 59.8 + - - +
90M SER* 2.7 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 34 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M GLN* 3.9 18.2 - - - -
20M ILE* 3.5 28.0 - - + -
21M SER 4.3 0.2 - - - -
22M CYS* 3.5 31.2 - - + -
32M MET* 4.3 11.5 + - + +
33M HIS* 1.3 82.7 - - - +
35M TYR* 1.3 63.9 + - - +
45M LEU* 3.6 6.8 - - - +
46M LEU* 2.9 26.4 + - + -
47M ILE* 2.8 40.8 + - + +
50M ALA* 4.9 4.4 + - - +
63M GLY* 5.6 0.2 - - - -
70M PHE* 4.5 5.0 - - + +
71M THR* 3.8 18.0 + - - -
72M LEU* 3.6 51.6 - - + -
85M TYR* 4.9 1.3 - - + -
86M PHE 3.2 21.3 - - - -
87M CYS* 3.7 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I LEU* 6.0 0.7 - - + -
105I TRP* 3.5 4.0 - - + +
106I PHE* 2.8 50.4 + + - -
109I TRP* 4.2 8.3 - + - -
33M HIS* 4.6 2.9 - - + -
34M TRP* 1.3 77.9 - - - +
36M GLN* 1.3 59.6 + - - +
37M GLN 4.2 0.2 - - - -
43M PRO* 4.0 24.7 - - + -
44M LYS 3.2 7.6 - - - +
45M LEU* 3.7 31.9 - - + -
46M LEU* 4.1 5.1 - - - +
84M ILE 3.9 0.2 - - - +
85M TYR* 3.2 9.2 - - - +
86M PHE* 2.8 45.8 + - + +
88M GLN* 2.5 44.4 + - + -
97M PHE* 3.9 17.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 36 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M TYR* 1.3 73.9 - - - +
37M GLN* 1.3 61.8 + - - +
38M LYS* 3.6 32.6 + - + +
42M GLN 4.1 1.0 - - - +
43M PRO* 4.3 0.7 - - - -
44M LYS* 2.7 59.0 + - + +
46M LEU* 3.7 25.1 - - + +
61M PHE* 4.3 9.3 - - - -
81M ASP* 4.3 14.6 + - - +
83M ALA* 3.9 11.0 - - + +
84M ILE 3.7 2.9 - - - -
85M TYR* 3.0 34.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I GLN* 3.0 41.9 + - - -
43I LYS* 5.0 2.6 - - - +
36M GLN* 1.3 75.1 - - - +
38M LYS* 1.3 63.4 + - - +
39M PRO* 4.1 0.5 - - - +
41M GLN 2.9 28.4 + - - +
42M GLN* 4.0 4.7 - - - +
43M PRO* 3.7 29.8 - - + +
83M ALA* 3.4 3.5 - - - +
84M ILE* 2.8 44.8 + - + +
86M PHE* 3.4 19.0 - - + -
----------------------------------------------------------
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