Contacts of the strand formed by residues 90 - 101 (chain B) 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 LYS 90 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS* 6.2 0.7 - - - +
33B GLN* 6.1 2.1 - - - +
83B ILE* 3.9 20.2 - - + -
84B CYS 3.7 2.0 - - - -
85B GLU* 3.6 39.9 - - + -
88B ASP 5.8 0.2 - - - -
89B GLN* 1.3 82.7 + - - +
91B GLU* 1.3 65.4 + - - +
92B GLU* 4.1 3.0 + - + +
512O NAG 5.6 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR 3.9 4.6 - - - +
16B CYS* 2.7 43.8 - - - +
17B THR* 3.4 25.8 + - - +
28B TRP* 5.5 0.2 - - - -
82B TYR 3.6 1.2 - - - +
83B ILE* 3.1 7.7 - - - +
84B CYS* 2.9 40.2 + - + +
86B VAL* 5.1 2.2 - - + -
89B GLN* 5.8 5.6 - - + -
90B LYS* 1.3 76.6 - - - +
92B GLU* 1.3 62.6 + - - +
93B VAL* 4.8 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LYS 4.3 17.6 + - - +
2B LYS* 3.7 20.3 + - - +
81B THR* 4.2 18.2 - - + +
82B TYR 3.4 2.5 - - - -
83B ILE* 3.9 26.2 - - + +
90B LYS* 4.1 3.6 + - + +
91B GLU* 1.3 72.4 - - - +
93B VAL* 1.3 66.3 - - - +
94B GLN 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS* 3.5 12.3 - - + +
4B VAL* 4.0 22.2 - - + -
14B LEU* 4.0 31.4 - - + -
15B THR 4.8 11.0 - - - +
28B TRP* 4.4 20.0 - - + -
81B THR* 3.6 2.2 - - - -
82B TYR* 2.9 45.7 + - + +
91B GLU* 4.8 7.6 - - + +
92B GLU* 1.3 81.2 - - - +
94B GLN* 1.3 61.9 + - - +
95B LEU 3.6 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LYS 6.0 0.4 - - - +
2B LYS 2.6 17.7 + - - +
3B VAL* 3.2 23.0 - - + +
4B VAL 2.7 32.3 + - - -
80B ASP 3.7 6.5 - - - +
81B THR* 3.3 26.1 + - + +
92B GLU 4.2 0.2 - - - -
93B VAL* 1.3 71.9 - - - +
95B LEU* 1.3 56.8 + - - +
96B LEU* 3.7 27.8 - - + +
164B ASN* 5.3 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 3.2 42.6 - - + +
6B GLY* 4.6 6.5 - - - +
12B VAL* 4.0 22.4 - - + -
14B LEU* 4.1 9.0 - - + -
71B ILE* 4.2 18.4 - - + -
74B LEU* 4.4 2.9 - - + -
78B ASP 3.5 19.7 - - - +
79B SER* 3.3 3.5 - - - -
80B ASP 2.8 39.6 + - - +
82B TYR* 4.0 19.5 - - + -
93B VAL 3.6 0.8 + - - +
94B GLN* 1.3 74.3 - - - +
96B LEU* 1.3 75.1 + - - +
97B VAL* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 3.9 23.6 - - + -
4B VAL 3.0 7.3 + - - -
5B LEU* 3.6 13.0 - - + +
6B GLY* 3.0 25.1 + - - +
79B SER* 4.0 5.6 - - - -
80B ASP 5.2 0.9 - - - +
94B GLN* 3.7 28.5 - - + +
95B LEU* 1.3 84.3 - - - +
97B VAL* 1.3 63.7 + - - +
98B PHE* 3.9 26.7 + - + -
121B PRO* 3.7 22.9 - - + -
122B PRO 5.4 4.5 - - - +
123B GLY 5.9 0.9 - - - -
124B SER* 4.8 8.1 - - - +
163B GLN* 4.9 5.2 - - + +
164B ASN* 4.6 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLY 3.2 12.6 - - - +
7B LYS 4.2 0.7 - - - -
8B LYS* 3.7 21.8 - - - -
74B LEU* 4.0 23.8 - - + -
75B LYS 3.1 34.8 - - - +
76B ILE* 3.6 16.5 - - + +
78B ASP 4.2 1.8 - - - -
79B SER* 3.0 26.5 + - - +
95B LEU* 4.3 7.9 - - + -
96B LEU* 1.3 77.0 - - - +
98B PHE* 1.3 62.6 + - - +
119B GLU 4.0 0.2 - - - +
121B PRO* 3.3 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.0 18.4 - - + -
6B GLY 3.3 6.9 + - - +
7B LYS* 3.5 1.6 - - - -
8B LYS* 2.8 25.0 + - - -
96B LEU* 3.9 19.1 - - + -
97B VAL* 1.3 77.3 - - - +
99B GLY* 1.3 60.7 + - - +
118B LEU* 4.7 6.1 - - + -
119B GLU 3.4 3.1 - - - +
120B SER* 3.5 24.5 - - - -
121B PRO* 3.5 20.2 - - + -
124B SER* 3.6 7.2 - - - -
126B PRO* 4.7 6.7 - - + -
161B VAL* 3.9 23.8 - - + -
163B GLN* 3.9 37.2 - - + -
168B VAL* 4.1 12.8 - - + -
170B PHE* 3.1 24.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS* 3.9 25.9 - - - +
76B ILE* 4.8 1.4 - - - +
98B PHE* 1.3 72.8 - - - +
100B LEU* 1.3 62.0 + - - +
101B THR* 4.1 2.2 - - - -
118B LEU* 3.3 8.5 - - - +
119B GLU* 2.9 40.2 + - - +
170B PHE* 3.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY* 1.3 74.2 - - - +
101B THR* 1.3 60.8 + - - +
102B ALA 4.1 0.7 + - - -
116B LEU* 4.6 19.3 - - + -
117B THR 3.2 11.4 - - - +
118B LEU* 3.8 25.4 - - + -
128B VAL* 4.1 11.9 - - + -
159B CYS* 3.7 41.1 - - + -
161B VAL* 4.4 1.8 - - + -
170B PHE* 3.6 39.6 - - + -
172B ILE* 4.5 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY 5.7 1.3 - - - -
100B LEU* 1.3 75.2 - - - +
102B ALA* 1.3 72.1 + - - +
115B THR 4.4 0.2 - - - +
116B LEU* 4.4 2.5 - - - -
117B THR* 2.9 36.4 + - - +
119B GLU* 5.4 10.3 - - + +
172B ILE* 5.0 2.0 - - - -
----------------------------------------------------------
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