Contacts of the strand formed by residues 92 - 100 (chain B) in PDB entry 4CMM
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 GLY 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 4.0 4.9 - - - -
43B LYS* 5.0 4.0 - - - -
90B HIS 3.9 0.8 + - - -
91B THR* 1.3 75.8 - - - +
93B ASN* 1.3 62.3 + - - -
94B TYR* 3.5 5.7 - - - -
110B GLU* 3.8 13.2 - - - -
111B LEU* 2.7 41.4 + - - +
1124B NAG 4.8 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS 5.1 0.2 - - - +
42B PHE* 3.5 7.7 - - - -
43B LYS* 3.5 29.1 + - + +
92B GLY* 1.3 71.2 - - - -
94B TYR* 1.3 59.6 + - - +
108B ILE* 3.6 21.0 - - + +
109B ILE 3.6 0.7 - - - -
110B GLU* 3.2 21.1 + - - +
1124B NAG 1.4 69.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
21B ILE* 3.6 33.0 - - + -
40B TRP* 3.9 25.6 - + + -
41B LYS 3.1 14.1 - - - +
42B PHE* 3.6 24.7 - + + -
47B ILE* 3.9 11.9 - - + -
63B PHE* 3.2 26.7 - + - -
80B LEU* 4.3 0.2 - - + -
82B MET* 3.6 11.9 - - + +
90B HIS* 2.6 30.2 + - - +
92B GLY 3.5 11.2 - - - -
93B ASN* 1.3 74.3 - - - +
95B THR* 1.3 62.9 + - - +
107B THR 4.0 0.2 - - - +
108B ILE* 3.3 6.1 - - - +
109B ILE* 2.8 38.0 + - - +
111B LEU* 3.7 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS 3.5 1.7 - - - +
40B TRP* 3.3 8.5 - - - -
41B LYS* 2.8 52.2 + - + +
94B TYR* 1.3 76.0 + - - +
96B CYS* 1.3 63.2 + - - +
97B GLU* 4.7 2.2 - - + +
106B GLU* 3.5 39.0 - - + +
107B THR 3.3 11.4 - - - +
108B ILE* 3.8 15.8 - - + +
----------------------------------------------------------
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 PHE* 4.0 3.6 - - - -
23B CYS* 2.0 48.5 - - + -
38B VAL* 5.0 0.9 - - - -
39B LYS 3.6 2.9 - - - -
40B TRP* 3.6 34.3 - - + -
78B ALA* 4.0 5.4 - - - -
94B TYR 4.3 0.2 + - - -
95B THR* 1.3 71.4 - - - +
97B GLU* 1.3 63.3 + - - +
98B VAL* 4.0 13.2 - - - -
106B GLU* 3.1 4.1 - - - -
107B THR* 2.8 37.2 + - + +
109B ILE* 4.2 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 2.8 36.0 + - - -
96A LYS* 2.9 32.4 + - - -
101A ASP* 5.3 0.2 - - - +
37B TYR* 3.8 0.9 - - - +
38B VAL* 3.3 5.7 - - - +
39B LYS* 2.8 69.8 + - + +
41B LYS* 4.6 9.8 + - + -
95B THR* 4.0 3.3 - - + -
96B CYS* 1.3 73.4 - - - +
98B VAL* 1.3 67.9 + - - +
99B THR* 4.2 3.2 + - - +
104B GLU* 4.6 2.9 - - + +
105B GLY 3.4 13.0 - - - +
106B GLU* 4.0 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 3.4 20.4 - - + +
4B PHE* 4.0 5.6 - - + -
25B VAL* 3.8 26.2 - - + -
28B MET* 4.0 21.5 - - + -
36B VAL* 4.1 6.3 - - + -
37B TYR 3.5 7.6 - - - +
38B VAL* 4.5 5.2 - - + -
73B LEU* 5.3 1.8 - - + -
78B ALA* 4.0 14.6 - - + -
96B CYS* 4.0 20.4 - - - -
97B GLU* 1.3 79.4 - - - +
99B THR* 1.3 68.5 + - - +
104B GLU* 3.4 1.0 - - - +
105B GLY* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.8 11.4 - - + -
34A GLY* 3.9 17.0 - - - +
35A PRO* 4.7 0.7 - - + -
96A LYS* 3.5 25.7 + - + +
2B LEU* 3.9 2.0 - - - -
35B GLU 4.2 0.2 - - - -
36B VAL* 3.2 10.7 - - - +
37B TYR* 2.9 42.5 + - - +
97B GLU* 4.2 3.6 + - - -
98B VAL* 1.3 75.7 + - - +
100B GLU* 1.3 62.3 + - - +
101B LEU 3.5 19.5 - - - +
103B ARG 3.3 12.6 - - - +
104B GLU* 4.1 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 3.1 31.8 + - - +
2B LEU* 3.6 17.2 - - + +
28B MET* 3.5 18.1 - - + +
29B GLU 2.8 22.2 + - - -
30B ALA* 2.9 31.4 + - + -
35B GLU* 3.3 8.1 - - - +
36B VAL* 4.6 1.3 - - + -
99B THR* 1.3 72.6 - - - +
101B LEU* 1.4 58.1 + - - +
102B THR 3.0 0.7 + - - -
103B ARG* 2.8 62.1 + - - +
----------------------------------------------------------
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