Contacts of the strand formed by residues 75 - 81 (chain A) in PDB entry 2CND
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 HIS 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.7 10.2 - - + +
31A ARG* 2.6 45.5 + - + +
32A PHE 2.9 16.2 - - - +
33A SER* 3.7 22.8 - - - -
34A LEU* 4.5 5.2 - - - +
41A LEU* 5.9 0.3 - - - +
72A GLU* 3.5 31.1 + - - +
73A ILE 3.4 11.4 + - - -
74A GLY* 1.3 88.5 + - - +
76A PHE* 1.4 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A CYS* 3.5 29.8 - - - -
30A PHE 3.9 0.3 - - - +
32A PHE* 2.9 66.8 + + + -
34A LEU* 3.5 23.8 - - + -
41A LEU* 3.5 33.9 - - + -
49A ILE* 3.9 17.9 - - + -
51A VAL* 5.9 0.2 - - + -
66A PRO* 4.5 4.7 - - + -
68A SER* 3.3 13.0 - - - +
75A HIS* 1.4 72.5 - - - +
77A ASP* 1.3 65.0 + - - +
78A LEU* 4.2 15.9 - - + -
112A VAL* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.9 25.5 - - + +
30A PHE 3.3 7.0 - - - +
31A ARG* 2.8 52.7 + - - +
66A PRO* 3.3 10.4 - - - +
67A THR* 3.1 31.4 + - - +
68A SER* 3.0 16.4 + - - +
76A PHE* 1.3 77.0 - - - +
78A LEU* 1.3 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG 3.8 0.2 - - - +
29A LEU* 3.6 7.4 - - - -
30A PHE* 3.0 31.1 + - + +
32A PHE* 3.6 34.1 - - + -
49A ILE* 4.5 2.0 - - + -
51A VAL* 3.9 26.9 - - + -
64A TYR* 4.1 22.9 - - + -
65A THR 4.8 0.7 - - - -
66A PRO* 4.0 28.7 - - + -
76A PHE* 4.2 10.8 - - + -
77A ASP* 1.3 83.6 - - - +
79A LEU* 1.3 61.0 + - - +
80A VAL* 3.6 19.2 + - + -
101A LEU* 5.1 4.0 - - + -
271A FAD 5.9 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.5 31.9 - - + -
27A VAL* 4.6 3.6 - - + -
28A ARG 3.8 4.7 - - - +
29A LEU* 4.2 12.1 - - + -
65A THR 5.7 0.4 + - - -
67A THR* 3.8 20.8 + - + +
77A ASP 4.3 0.4 - - - -
78A LEU* 1.3 68.4 - - - +
80A VAL* 1.3 54.7 + - - +
81A LYS 4.2 0.2 + - - -
146A SER* 5.2 0.7 - - - -
149A THR* 4.4 6.6 - - + +
182A LEU* 4.0 34.6 - - + +
183A LEU* 3.5 43.3 - - + +
271A FAD 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.7 4.5 - - - +
28A ARG* 3.1 32.3 + - - +
30A PHE* 3.2 39.5 - - + -
64A TYR* 4.0 22.2 - - + +
78A LEU* 3.6 18.1 + - + -
79A LEU* 1.3 78.7 - - - +
81A LYS* 1.3 64.3 + - - +
82A VAL* 3.6 9.2 + - + +
98A THR* 3.7 29.8 - - + +
101A LEU* 4.7 5.6 - - + -
182A LEU* 6.3 0.9 - - - -
271A FAD 3.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP* 3.0 36.6 + - - +
27A VAL* 3.9 16.6 - - + +
79A LEU 4.2 0.4 - - - -
80A VAL* 1.3 70.7 - - - +
82A VAL* 1.3 62.8 + - - +
83A TYR* 3.5 33.1 + - + +
98A THR* 3.4 15.8 - - - +
146A SER* 4.4 17.3 - - - +
180A ASP* 4.0 24.3 + - - +
182A LEU* 4.9 15.0 - - + +
271A FAD 3.1 17.2 + - - +
----------------------------------------------------------
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