Contacts of the strand formed by residues 85 - 92 (chain M) in PDB entry 4R2G
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 85 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M TYR* 4.2 2.8 + - - -
36M TYR 3.7 0.7 - - - +
37M GLN* 3.5 3.6 - - - -
38M HIS* 2.8 46.1 + - + +
40M PRO* 5.3 7.4 - - - +
84M ALA* 1.3 82.9 - - - +
86M TYR* 1.3 61.5 + - - +
87M TYR* 3.9 20.7 + - + -
101M ALA* 4.2 14.7 - - + +
102M THR 3.2 6.3 - - - +
103M ARG* 2.6 52.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ILE* 3.7 25.6 - - + -
35M TRP* 4.7 13.2 - + + -
36M TYR 3.5 2.0 - - - +
37M GLN* 2.9 25.6 + - + -
47M LEU* 3.6 26.0 - - + -
62M PHE* 4.2 4.3 - + - -
73M LEU* 3.7 16.6 - - + -
75M ILE* 3.7 21.3 - - + +
82M ASP* 2.6 35.1 + - - +
84M ALA* 3.8 17.5 - - + -
85M ASP* 1.3 78.0 - - - +
87M TYR* 1.3 62.5 + - - +
88M CYS 4.1 0.5 + - - -
100M GLY 4.5 0.3 - - - +
101M ALA* 4.0 1.4 - - - -
102M THR* 2.8 38.8 + - - +
104M LEU* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M TYR* 3.7 11.0 + + - -
34M GLN 3.7 0.3 - - - +
35M TRP* 3.2 12.4 - - - -
36M TYR* 2.9 49.5 + - + +
38M HIS* 4.0 13.3 - + + -
85M ASP* 3.9 26.6 + - + -
86M TYR* 1.3 75.2 - - - +
88M CYS* 1.3 61.6 + - - +
89M HIS 3.8 0.6 + - - -
98M PHE* 3.9 27.6 - - + +
99M GLY 3.9 7.6 - - - -
100M GLY 3.3 24.2 - - - -
101M ALA* 3.7 9.3 - - + +
39N GLN* 5.6 0.9 + - - -
44N GLY* 3.5 12.4 - - - -
45N LEU* 3.5 54.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 88 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M CYS* 2.1 52.0 - - + -
24M GLY 5.2 0.9 - - - +
25M ARG* 2.7 28.8 + - - -
33M VAL* 3.5 21.5 - - - -
34M GLN 3.5 3.4 - - - -
35M TRP* 3.4 33.5 - - + -
71M ALA* 4.8 0.2 - - - -
86M TYR 4.1 0.4 + - - -
87M TYR* 1.3 70.4 - - - +
89M HIS* 1.3 51.3 + - - +
90M MET 3.2 2.9 + - - -
98M PHE 3.3 8.1 + - - +
99M GLY* 4.9 0.2 - - - -
100M GLY 4.9 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 89 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M ARG* 3.6 1.6 - - - +
33M VAL* 3.5 3.4 - - - -
34M GLN* 2.8 44.2 + - + +
36M TYR* 3.7 22.2 - - + -
87M TYR 3.8 2.0 - - - -
88M CYS* 1.3 70.1 - - - +
90M MET* 1.3 59.9 + - - +
91M TRP* 3.4 31.3 + - - -
95M SER* 3.3 31.8 - + - -
97M SER 3.3 23.7 + - - -
98M PHE* 3.7 30.7 + + + -
47N TRP* 4.0 11.3 - + - -
100N TYR* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 90 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M CYS* 3.7 16.6 - - - -
25M ARG* 3.2 62.5 + - + +
26M GLN* 4.6 0.9 - - - +
27M ALA* 3.5 37.9 - - + +
31M ARG* 4.1 1.6 - - - -
33M VAL* 3.6 29.4 - - + -
71M ALA* 3.9 12.8 - - + -
88M CYS 3.2 0.6 + - - -
89M HIS* 1.3 70.1 + - - +
91M TRP* 1.3 70.5 + - - +
92M ASP* 4.3 3.3 + - + +
95M SER* 3.2 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 91 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M ARG* 3.3 7.4 - - - +
32M ALA* 2.9 45.3 + - + +
34M GLN* 3.3 17.1 - - - +
89M HIS* 3.4 44.7 + + - -
90M MET* 1.3 77.8 - - - +
92M ASP* 1.3 65.2 + - - +
95M SER* 3.5 77.2 - + + -
47N TRP* 3.7 11.0 - + - -
100N PHE* 3.5 68.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M ALA* 3.5 12.7 - - + -
28M LEU* 2.6 34.1 + - - +
29M GLY 3.8 19.3 - - - +
30M SER 3.7 6.1 - - - +
90M MET* 4.3 4.3 + - - +
91M TRP* 1.3 76.7 - - - +
93M SER* 1.3 62.6 + - - +
94M ARG 3.7 4.7 - - - -
95M SER* 2.5 54.9 + - - +
100N PHE* 3.4 17.6 + - - +
----------------------------------------------------------
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