Contacts of the strand formed by residues 79 - 91 (chain B) in PDB entry 4GJC
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 THR 79 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.6 27.1 - - + -
73B LEU 3.4 13.5 - - - +
74B ARG* 3.8 21.2 + - + +
75B TYR 4.7 0.9 + - - -
78B GLY* 1.4 75.0 + - - -
80B VAL* 1.3 66.9 + - - +
81B SER* 4.8 2.7 - - - +
106B GLU* 5.6 0.9 - - - +
108B PRO* 3.1 31.7 - - - +
112B PHE* 4.1 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TRP* 4.0 26.0 - - + +
72B THR* 3.4 3.1 - - - +
73B LEU* 2.8 58.1 + - + +
75B TYR* 4.0 6.5 - - + -
79B THR* 1.3 70.2 - - - +
81B SER* 1.3 64.5 + - - +
104B VAL* 3.9 23.6 - - + -
106B GLU* 3.4 16.4 - - - +
107B MET* 4.1 8.5 - - + -
112B PHE* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU 3.4 10.1 - - - -
72B THR* 3.6 18.0 + - - +
73B LEU* 6.3 0.2 - - - -
79B THR* 4.8 2.8 - - - +
80B VAL* 1.3 77.6 + - - +
82B GLY* 1.3 59.9 + - - +
104B VAL* 3.7 7.3 - - - -
105B THR* 3.0 21.9 + - - -
106B GLU* 3.0 40.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU* 3.4 8.5 - - - +
71B LEU* 2.8 39.5 + - - +
81B SER* 1.3 76.5 - - - +
83B PHE* 1.3 57.6 + - - -
103B GLU 3.1 15.7 - - - -
104B VAL* 4.2 2.1 - - - +
105B THR* 3.7 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B SER* 4.1 0.4 - - - -
44B LYS* 3.6 26.5 - - + -
64B TYR* 4.8 7.0 - - - -
66B HIS* 5.7 3.1 - + - -
68B GLY* 3.5 30.3 - - - +
69B THR 3.2 7.0 - - - +
70B GLU* 4.5 4.9 - - + -
71B LEU* 3.6 5.6 - - - -
82B GLY* 1.3 75.2 - - - +
84B LEU* 1.3 69.1 + - - +
85B SER* 3.4 18.6 - - - -
102B GLY* 3.5 0.5 - - - -
103B GLU* 2.8 60.6 + - + -
105B THR* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 5.5 0.9 - - - +
67B ASN* 3.4 9.4 + - - +
68B GLY 2.8 28.4 + - - -
69B THR* 2.8 36.4 + - + +
71B LEU* 4.1 23.6 - - + -
83B PHE* 1.3 74.7 - - - +
85B SER* 1.3 63.3 + - - +
100B MET* 3.6 29.2 - - + -
101B PHE* 3.4 26.2 - - - +
102B GLY 4.1 2.2 - - - +
131B GLY* 5.4 5.6 - - - +
133B VAL* 3.7 30.7 - - + -
1000B NAG 5.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.6 17.4 + - - -
65B LYS 4.0 4.9 - - - -
67B ASN* 4.5 2.7 - - - +
83B PHE* 3.4 10.0 - - - -
84B LEU* 1.3 74.7 + - - +
86B GLN* 1.3 61.8 + - - +
100B MET* 3.3 8.6 - - - +
101B PHE* 2.8 50.8 + - - +
103B GLU* 2.6 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER 5.3 0.3 - - - +
64B TYR* 3.4 5.4 - - - -
65B LYS* 2.8 66.2 + - + +
66B HIS 5.8 0.4 - - - +
85B SER* 1.3 75.3 - - - +
87B ASP* 1.3 67.4 + - - +
97B THR* 3.5 29.4 - - + +
99B GLN 3.4 14.8 - - - +
100B MET* 3.8 22.1 - - + +
101B PHE* 4.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 3.7 6.7 - - + -
21B GLY* 3.2 11.1 - - - -
56B PHE* 3.4 13.1 - - + -
61B SER* 2.7 28.2 + - - -
63B SER* 2.6 33.7 + - - -
64B TYR* 3.5 12.9 - - - +
86B GLN* 1.3 76.1 - - - +
88B ILE* 1.3 73.7 + - - +
89B ILE* 3.7 2.5 + - - +
97B THR* 3.7 4.8 - - - -
99B GLN* 2.9 31.9 + - - +
101B PHE* 3.7 17.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY 3.7 0.9 - - - +
20B ILE* 3.4 3.8 - - - +
21B GLY 2.9 31.1 + - - +
22B THR* 4.3 7.9 - - - +
63B SER* 3.7 28.5 - - - +
87B ASP* 1.3 82.8 + - - +
89B ILE* 1.3 63.2 + - - +
90B THR* 4.9 4.5 + - - +
95B THR* 3.5 34.1 - - + +
96B VAL 3.4 8.1 - - - +
97B THR* 3.9 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 4.0 26.2 - - + -
19B GLY 3.2 8.3 - - - +
20B ILE* 3.9 23.8 - - + -
38B VAL* 3.9 22.4 - - + -
87B ASP 4.2 2.7 - - - +
88B ILE* 1.3 77.7 - - - +
90B THR* 1.4 66.1 + - - +
91B VAL* 4.0 1.4 + - + -
94B ILE 3.8 0.5 - - - +
95B THR* 3.5 1.4 - - - -
96B VAL* 2.7 44.9 + - - +
99B GLN* 3.7 32.5 - - + -
101B PHE* 4.2 9.4 - - + -
136B ILE* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU 4.5 0.2 - - - +
18B ILE* 3.4 9.5 - - - +
19B GLY* 2.8 40.3 + - - -
21B GLY 5.4 2.1 + - - -
24B PRO* 4.5 14.4 - - + +
88B ILE* 4.9 5.2 + - - +
89B ILE* 1.4 71.7 - - - +
91B VAL* 1.3 60.5 + - - +
92B GLY 4.1 1.3 + - - +
93B GLY* 4.6 13.7 - - - +
94B ILE 3.3 13.0 - - - +
95B THR* 3.7 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 3.0 11.2 + - - -
4B VAL* 3.7 21.3 - - + -
17B GLU 5.0 1.3 - - - -
18B ILE* 4.1 11.0 - - + -
31B PHE* 4.3 20.2 - - + -
89B ILE* 4.5 5.4 - - + +
90B THR* 1.3 75.0 - - - +
92B GLY* 1.3 64.8 + - - +
94B ILE* 2.8 30.0 + - + +
96B VAL* 4.8 2.2 - - + -
136B ILE* 4.1 20.0 - - + -
140B ILE* 4.1 23.6 - - + -
167B LEU* 3.7 16.9 - - + +
----------------------------------------------------------
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