Contacts of the strand formed by residues 88 - 94 (chain D) in PDB entry 2CHS
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 CYS 88 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ALA* 4.6 5.2 - - - -
10D THR 3.4 11.0 - - - -
11D THR* 4.3 1.1 - - + -
48D SER 3.8 0.3 - - - +
49D ALA* 3.4 4.9 - - - -
50D THR* 2.9 29.9 + - + +
53D LEU* 4.0 0.9 - - - +
78D GLU* 5.7 0.2 - - - +
85D LEU* 3.4 48.7 - - + +
86D LYS 3.9 3.4 - - - +
87D LYS* 1.3 74.9 - - - +
89D ILE* 1.3 63.8 + - - +
90D ARG* 3.3 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ALA* 3.3 2.9 - - - -
10D THR* 2.8 45.9 + - + +
12D VAL* 3.9 24.2 - - + -
20D ILE* 3.6 22.7 - - + +
24D THR* 3.4 29.4 - - + +
27D LEU* 4.1 5.6 - - + +
47D LEU* 4.1 15.3 - - + -
48D SER 3.3 9.9 - - - +
49D ALA* 4.9 3.1 - - + -
53D LEU* 3.7 16.4 - - + -
58D PRO* 4.0 17.3 - - + -
87D LYS 4.7 0.9 - - - +
88D CYS* 1.3 75.0 - - - +
90D ARG* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ARG* 3.5 28.0 - - - +
8D GLY 3.3 4.5 - - - -
9D ALA* 4.1 5.8 - - + +
27D LEU* 5.3 0.2 - - - -
47D LEU* 3.3 6.0 - - - +
48D SER* 2.9 42.6 + - - +
50D THR* 4.0 5.7 - - - +
76D MET* 5.7 0.3 - - - +
78D GLU* 3.3 40.8 + - - +
85D LEU* 4.3 17.4 + - - +
88D CYS* 3.3 38.7 + - - +
89D ILE* 1.3 77.4 - - - +
91D VAL* 1.3 61.2 + - - +
115D LEU* 5.5 7.5 - - - +
57F PHE* 3.8 24.2 - - - -
74F THR* 4.1 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE 4.8 0.7 - - - +
7D ARG* 3.0 21.8 + - - -
8D GLY* 2.9 38.4 + - - +
27D LEU* 4.1 9.2 - - + -
28D LEU* 4.1 8.1 - - + -
31D ILE* 3.6 18.4 - - + -
45D MET* 3.6 29.4 - - + -
46D LEU 3.3 11.2 - - - +
47D LEU* 3.7 15.0 - - + -
90D ARG* 1.3 74.0 - - - +
92D MET* 1.3 66.7 + - - +
93D MET* 4.1 5.6 - - + +
74F THR* 5.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D GLY* 3.5 16.2 - - - -
6D ILE 3.5 36.8 - - - +
7D ARG* 3.7 15.7 - - + -
45D MET* 3.5 2.3 - - - -
46D LEU* 3.0 42.4 + - + +
76D MET* 6.1 0.2 - - - +
91D VAL* 1.3 75.8 - - - +
93D MET* 1.3 57.3 + - - +
94D THR* 4.2 1.8 + - - +
44F GLN* 3.9 35.0 - - + +
45F MET 4.5 5.6 - - - +
46F LEU* 4.8 4.5 - - + -
72F PRO* 3.6 23.6 - - + +
74F THR* 4.2 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ARG 3.8 0.5 - - - +
5D GLY* 3.3 3.0 - - - -
6D ILE* 2.7 46.3 + - + +
28D LEU* 4.3 13.5 - - + -
31D ILE* 4.1 27.8 - - + -
32D ILE* 4.5 6.7 - - + -
37D THR* 4.2 9.9 - - - -
42D VAL* 4.0 17.5 - - + -
44D GLN 3.8 3.4 - - - -
45D MET* 4.0 22.2 - - + -
68D TRP* 3.5 34.3 - - + -
91D VAL* 4.5 4.5 - - + -
92D MET* 1.3 71.7 - - - +
94D THR* 1.3 60.5 + - - +
95D VAL* 4.1 17.9 + - + -
44F GLN* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ILE* 3.6 31.9 - - + -
4D ARG 3.6 3.8 - - - +
42D VAL* 3.6 2.6 - - - +
43D VAL* 2.8 43.5 + - + -
44D GLN* 3.0 25.7 + - + +
92D MET* 4.8 2.9 + - - +
93D MET* 1.3 71.0 - - - +
95D VAL* 1.3 63.8 + - - +
94E THR* 6.2 0.7 - - + -
43F VAL* 4.2 4.0 - - + -
44F GLN* 2.6 33.9 + - - +
94F THR* 6.3 0.2 - - + -
----------------------------------------------------------
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