Contacts of the strand formed by residues 94 - 103 (chain J) in PDB entry 3MGO
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 94 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J THR* 4.1 2.9 - - + -
11J SER 3.4 7.4 - - - +
12J VAL* 4.0 21.7 - - + +
92J SER* 5.6 0.2 + - - -
93J HIS* 1.3 77.0 + - - +
95J VAL* 1.3 65.4 + - - +
96J GLN* 3.9 26.0 - - + +
117J ALA 3.8 0.5 - - - +
118J TYR* 3.5 6.6 - - - -
119J ASP* 2.8 40.6 + - - -
0K MET* 5.9 0.9 - - - +
31K HIS* 4.3 16.7 - - + -
32K PRO* 4.5 13.3 - - - +
33K SER* 5.1 0.9 + - - -
62K PHE* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J PHE 3.7 0.7 - - - +
10J THR* 3.5 2.3 - - - -
11J SER* 2.7 48.3 + - - +
74J HIS* 3.7 23.2 - - + +
77J ASP* 5.0 6.3 - - + -
78J LEU* 3.5 29.6 - - + +
81J LEU* 3.6 30.7 - - + -
94J THR* 1.3 74.6 - - - +
96J GLN* 1.3 65.5 + - - +
116J TYR* 4.1 21.5 - - + -
117J ALA 3.6 4.9 - - - +
118J TYR* 3.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J PHE 3.1 9.6 - - - +
10J THR* 4.3 3.4 - - - +
94J THR* 3.9 11.0 - - + +
95J VAL* 1.3 82.4 - - - +
97J ARG* 1.3 60.7 + - - +
116J TYR* 3.3 7.4 - - - -
117J ALA* 2.9 35.8 + - - +
120J GLY* 4.0 11.3 + - - -
31K HIS* 2.8 26.9 + - - -
56K PHE* 3.3 29.3 - - + -
60K TRP* 2.9 44.5 + - + +
62K PHE* 3.6 15.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J PHE* 2.7 52.5 + - + +
70J HIS* 3.2 32.0 + - - -
74J HIS* 3.5 29.0 + - - +
96J GLN* 1.3 74.1 - - - +
98J MET* 1.3 67.6 + - - +
99J TYR* 4.1 12.9 - - + -
114J HIS* 3.1 32.5 + - - -
115J GLN 3.3 8.5 - - - +
116J TYR* 3.0 38.4 + - + -
56K PHE* 3.5 6.2 - - - -
60K TRP* 4.3 0.7 - - - -
2L TYR* 5.2 4.9 - - - -
6L THR* 3.6 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 98 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ARG* 3.7 23.8 - - - +
7J TYR 3.3 8.7 - - - +
8J PHE* 3.5 36.8 - - + -
97J ARG* 1.3 80.0 - - - +
99J TYR* 1.3 71.8 + - - +
113J TYR* 4.0 17.5 - - + -
114J HIS* 3.3 2.3 - - - -
115J GLN* 2.8 66.7 + - - +
56K PHE* 4.1 9.0 - - + -
58K LYS* 6.2 6.1 - - + -
60K TRP* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ARG* 3.5 2.8 - - - +
7J TYR* 2.9 41.4 + + + -
9J PHE* 3.3 24.9 - + - -
70J HIS* 3.0 27.3 + - - -
97J ARG* 4.1 16.6 - - - -
98J MET* 1.3 83.3 - - - +
100J GLY* 1.3 61.4 + - - +
113J TYR 3.2 17.7 - - - +
114J HIS* 3.7 23.8 - + + +
156J LEU* 5.8 1.1 - - + -
159J TYR* 3.4 37.7 - + - -
160J LEU* 4.7 2.7 - - + -
1L LEU* 3.4 11.8 - - - +
2L TYR* 3.1 24.3 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J MET 3.0 14.6 - - - -
6J ARG* 3.7 8.3 - - - -
7J TYR* 6.0 0.9 - - - -
99J TYR* 1.3 81.2 - - - +
101J CYS* 1.3 61.2 + - - -
112J GLY* 3.5 0.3 - - - -
113J TYR* 2.9 31.0 + - - +
159J TYR* 5.6 0.4 - - - -
160J LEU* 3.4 10.7 - - - +
164J CYS* 3.9 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 101 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J SER* 3.1 5.5 - - - -
5J MET* 3.0 29.9 + - - -
6J ARG* 3.4 1.5 - - - +
100J GLY* 1.3 73.9 - - - +
102J ASP* 1.3 64.9 + - - +
109J PHE* 4.4 2.9 - - + -
111J ARG 3.3 8.7 - - - +
112J GLY* 4.8 0.2 - - - -
160J LEU 3.7 17.3 - - - +
164J CYS* 2.0 60.1 - - + -
165J VAL* 3.6 14.1 - - + -
168J LEU* 4.1 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 102 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J SER* 5.3 3.4 - - - +
3J HIS 3.5 4.5 - - - +
4J SER* 2.9 12.3 - - - -
6J ARG* 2.7 35.4 + - - -
101J CYS* 1.3 72.3 - - - +
103J VAL* 1.3 65.9 + - - +
109J PHE* 3.9 2.4 - - - -
110J LEU* 2.8 28.1 + - + -
111J ARG* 2.7 42.1 + - + +
113J TYR* 2.8 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J SER* 2.6 27.7 + - - -
3J HIS* 2.8 40.9 + - + +
101J CYS 5.2 0.2 - - - -
102J ASP* 1.3 80.2 - - - +
104J GLY* 1.3 60.3 + - - +
107J TRP* 3.7 22.7 - - + +
108J ARG 3.2 21.5 - - - +
109J PHE* 4.0 5.4 - - - -
110J LEU* 4.1 3.6 - - - -
165J VAL* 4.0 19.1 - - + +
168J LEU* 3.7 25.8 - - + -
169J ARG* 6.0 1.8 - - + -
172J LEU* 5.1 1.8 - - + -
----------------------------------------------------------
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