Contacts of the strand formed by residues 85 - 91 (chain A) in PDB entry 4QMW
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 TYR 85 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN 5.7 1.0 + - - -
71A ILE* 3.7 13.2 - - + +
74A LEU* 3.6 47.3 - - + +
75A SER* 3.5 35.8 - - - -
77A CYS 5.5 2.5 + - - +
83A THR 3.7 0.9 + - - +
84A LYS* 1.3 89.0 + - - +
86A TYR* 1.3 64.7 + - - +
87A GLY* 3.5 24.2 - - - -
88A SER* 2.8 36.6 + - - -
97A ILE* 4.1 9.0 - - + -
98A ILE 4.0 6.1 - - - -
99A MET* 4.6 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 4.1 19.7 - + + -
43A ASP* 3.5 21.4 + - - -
46A THR* 5.5 0.2 + - - -
48A LYS* 4.2 24.8 + - - +
49A VAL 4.9 1.4 + - - -
50A VAL* 3.6 24.8 - - + +
84A LYS* 3.8 27.8 + - + +
85A TYR* 1.3 78.5 - - - +
87A GLY* 1.3 59.0 + - - +
89A TYR* 4.7 6.9 + - - +
98A ILE* 2.8 27.2 + - + +
99A MET* 3.6 27.8 - - - -
100A GLU* 3.8 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN 6.0 0.4 - - - -
17A LYS* 5.9 2.9 - - - -
85A TYR* 3.5 22.2 - - - -
86A TYR* 1.3 83.1 - - - +
88A SER* 1.3 62.9 + - - -
89A TYR* 3.7 12.5 - - - -
96A TRP 3.7 0.7 - - - +
98A ILE* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET* 5.6 0.9 - - - -
15A ASN 5.3 2.6 + - - -
16A LEU* 3.4 13.4 - - - +
17A LYS* 2.9 26.4 + - - +
71A ILE* 3.6 27.0 - - - +
85A TYR* 2.8 26.8 + - - -
87A GLY* 1.3 72.4 + - - -
89A TYR* 1.3 64.7 + - - +
95A LEU* 3.9 17.7 - - - -
96A TRP 3.2 4.9 - - - -
97A ILE* 3.9 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.9 3.8 - - - -
17A LYS* 3.3 33.4 - - + +
18A ALA 3.7 16.2 - - - -
20A PRO* 3.6 34.3 - - + -
23A LEU* 3.9 22.7 - - + +
24A PHE* 3.5 21.5 - + - -
86A TYR 4.7 6.4 + - - -
87A GLY* 3.7 24.9 - - - -
88A SER* 1.3 78.2 - - - +
90A LEU* 1.3 61.9 + - - +
91A LYS 3.8 0.2 + - - -
95A LEU* 3.5 4.4 - - - +
96A TRP* 2.8 41.8 + - + +
98A ILE* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.7 24.1 - - + +
17A LYS 2.8 15.8 + - - +
18A ALA* 3.7 7.4 - - + +
19A ASP 3.7 20.4 + - - -
20A PRO* 3.7 0.9 - - - +
57A LEU* 5.4 10.5 - - + -
89A TYR* 1.3 73.2 - - - +
91A LYS* 1.3 61.1 + - - +
92A ASP 3.4 20.9 - - - +
93A THR 4.9 1.6 - - - -
94A LYS 3.4 20.0 - - - +
95A LEU* 4.9 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 3.9 21.3 - - + -
21A GLU* 3.2 30.7 - - - +
89A TYR 3.8 0.6 + - - -
90A LEU* 1.3 75.4 - - - +
92A ASP* 1.3 79.4 + - - +
94A LYS* 2.9 38.6 + - + +
96A TRP* 3.7 37.2 - - + +
----------------------------------------------------------
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