Contacts of the strand formed by residues 92 - 101 (chain B) in PDB entry 5MY4
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 ALA 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 3.9 17.9 - - + -
39B GLN 3.5 31.2 - - - +
40B ALA* 3.9 3.6 - - + +
41B PRO* 5.2 2.0 - - - -
90B ASP 3.2 9.6 + - - +
91B THR* 1.3 80.0 - - - +
93B MET* 1.3 64.9 + - - +
94B TYR* 3.4 6.1 - - + -
117B SER* 3.8 3.9 - - - -
118B VAL 2.9 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL 4.0 0.3 - - - +
38B ARG* 3.0 4.3 - - - -
39B GLN* 2.7 43.9 + - + +
41B PRO* 5.9 0.4 - - - +
92B ALA* 1.3 71.6 - - - +
94B TYR* 1.3 58.3 + - - +
95B TYR* 3.4 39.1 + - + +
114B GLN 4.0 4.9 - - - +
115B GLY* 3.5 30.3 - - - +
116B THR 3.6 7.6 - - - -
117B SER* 3.8 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU* 3.6 6.2 - - - +
20B LEU* 3.6 27.8 - - + -
36B TRP* 4.4 6.8 - + + -
37B VAL 3.6 3.1 - - - -
38B ARG* 3.0 40.4 + - + -
48B VAL* 4.5 7.4 - - + -
68B PHE* 4.5 4.9 - + - -
81B LEU* 4.2 13.0 - - + -
83B MET* 3.3 25.9 - - + +
90B ASP* 2.6 30.6 + - - +
92B ALA* 3.4 20.4 - - + -
93B MET* 1.3 72.7 - - - +
95B TYR* 1.3 61.9 + - - +
115B GLY* 3.2 2.9 - - - -
116B THR* 2.9 39.0 + - + +
118B VAL* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLN* 3.4 10.6 + - - -
47A GLN 4.1 2.3 + - - -
48A SER* 3.4 25.3 + - - -
49A PRO* 4.2 6.7 - - + -
6B GLU* 3.6 2.5 - - - +
36B TRP* 3.3 11.6 - - - -
37B VAL* 2.5 53.8 + - + +
39B GLN* 3.0 40.5 + - + -
45B PRO* 5.7 0.4 - - + -
93B MET* 3.4 29.2 - - + +
94B TYR* 1.3 73.4 - - - +
96B CYS* 1.3 64.0 + - - +
112B TRP* 3.9 30.1 - + + -
113B GLY 3.4 17.7 - - - +
114B GLN 3.6 10.1 - - - -
115B GLY* 3.6 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.7 7.3 - - + +
6B GLU* 3.2 14.4 + - + +
22B CYS* 2.0 55.4 - - + -
34B MET* 3.4 24.5 - - - -
35B ALA 3.5 4.9 - - - -
36B TRP* 3.8 11.7 - - + -
79B LEU* 3.6 5.4 - - + -
95B TYR* 1.3 73.2 - - - +
97B ALA* 1.3 59.9 + - - +
112B TRP* 3.3 3.6 - - - +
113B GLY 3.0 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.0 0.4 - - - -
34B MET* 3.5 7.3 - - - +
35B ALA* 2.7 43.0 + - + +
37B VAL* 4.5 6.7 - - + -
96B CYS* 1.3 77.3 - - - +
98B ARG* 1.3 62.4 + - - +
109B MET* 4.1 27.1 - - + -
111B TYR 3.2 9.9 - - - +
112B TRP* 4.1 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 3.7 9.3 - - - +
4B LEU* 3.8 8.3 - - + +
27B PHE* 3.4 53.9 - - + +
32B TYR* 3.7 43.6 + - + -
34B MET* 3.7 22.9 - - - -
97B ALA* 1.3 72.1 - - - +
99B TYR* 1.3 64.1 + - - +
100B ASP* 4.3 4.0 + - - -
109B MET* 3.1 6.1 - - - -
110B ASP* 2.8 62.8 + - - +
111B TYR* 2.8 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 5.1 1.5 - - - -
101A PRO* 3.3 15.8 - - - +
32B TYR* 3.2 21.1 - - - +
33B GLY 3.0 25.0 + - - +
34B MET 4.5 1.3 - - - -
35B ALA* 3.7 22.0 - - + -
47B TRP* 4.7 0.9 - - - -
50B PHE* 3.5 24.5 - + - -
97B ALA 3.8 1.4 + - - -
98B ARG* 1.3 74.3 - - - +
100B ASP* 1.3 61.0 + - - +
101B TYR* 4.9 0.2 - - - -
106B ASP* 3.6 41.0 - - + +
107B TYR 4.1 0.4 - - - -
108B VAL* 3.3 20.0 - - - -
109B MET* 3.4 33.3 - - + +
1C PCA 2.8 28.6 + - - -
2C PHE* 3.2 14.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 6.2 0.2 - - - -
32B TYR* 3.4 21.3 + - - -
98B ARG* 4.0 3.9 + - - -
99B TYR* 1.3 72.9 - - - +
101B TYR* 1.3 79.6 + - - +
102B ASP* 4.6 3.1 - - - +
106B ASP* 3.3 6.3 - - - -
107B TYR* 3.0 46.4 + - + -
108B VAL* 2.8 26.1 + - + +
110B ASP* 3.3 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASP* 3.3 29.8 + - - +
32B TYR* 3.7 30.4 + + - -
100B ASP* 1.3 85.8 + - - +
102B ASP* 1.3 77.1 + - - +
103B ASN* 3.8 20.9 - - - +
105B LEU 3.3 20.2 - - - +
106B ASP* 3.4 13.0 - - - +
107B TYR* 3.7 3.6 - - - -
4C HIS* 3.3 32.5 + + + +
----------------------------------------------------------
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