Contacts of the strand formed by residues 3 - 9 (chain B) in PDB entry 5OND
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 SER 3 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.3 17.0 + - - +
2B GLN* 1.3 76.8 + - - +
4B TRP* 1.3 61.4 + - - +
5B TYR* 3.5 29.3 + - - -
58B GLU* 3.1 10.3 - - - -
59B PHE 3.0 31.5 + - - +
61B PRO* 4.9 1.0 - - - +
87B ILE* 4.0 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.3 27.3 - - - +
45A ALA* 3.7 30.3 - - + -
3B SER* 1.3 72.3 - - - +
5B TYR* 1.3 59.8 + - - +
27B ASN* 4.1 6.3 - - + -
29B LEU* 4.0 12.8 - - + -
56B PHE* 3.8 24.9 - - + -
57B VAL* 3.3 37.7 - - - -
58B GLU* 3.2 29.2 + - + -
87B ILE* 3.4 9.4 - - - +
88B VAL* 2.7 43.0 + - + +
90B SER* 5.1 9.2 - - - -
93B ILE* 3.5 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SER* 3.5 34.7 - - - -
4B TRP* 1.3 74.1 - - - +
6B LEU* 1.3 62.4 + - - +
56B PHE* 3.3 8.5 - - - +
57B VAL* 2.7 41.2 + - + -
59B PHE* 3.4 38.6 - + - -
61B PRO* 3.1 30.1 - - + +
66B THR* 4.9 4.9 - - + +
78B PHE* 4.0 13.7 - + + -
85B PRO* 3.8 25.1 - - + -
86B ALA 3.4 20.9 - - - +
87B ILE* 3.7 24.0 - - + +
88B VAL* 3.8 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 1.3 74.7 - - - +
7B LEU* 1.3 57.4 + - - +
54B TYR* 3.8 26.7 - - + -
55B LEU 3.7 15.0 - - - +
56B PHE* 3.6 29.8 - - + -
78B PHE* 3.6 4.9 - - - +
79B VAL* 2.7 43.9 + - + +
86B ALA* 4.3 4.5 + - + +
88B VAL* 3.9 12.6 - - + +
142B LEU* 3.6 24.0 - - + -
143B LEU* 3.7 24.9 - - + -
146B ILE* 3.8 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 1.3 74.0 - - - +
8B TYR* 1.3 64.6 + - - +
9B CYS* 5.0 2.0 - - - -
21B LEU* 3.8 19.1 - - + -
54B TYR* 3.2 14.5 - - - -
55B LEU* 2.9 41.4 + - + +
57B VAL* 3.6 32.8 - - + -
69B ILE* 3.8 16.6 - - + -
75B VAL* 3.9 15.9 - - + -
77B HIS 3.5 5.6 - - - +
78B PHE* 3.5 49.4 - - + +
79B VAL 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 1.3 74.7 - - - +
9B CYS* 1.3 74.0 + - - +
10B LYS* 5.7 0.4 - - - -
11B ARG* 5.5 8.9 - - - -
52B PRO 3.9 2.1 + - - -
53B ASN* 3.6 31.3 + - + +
54B TYR* 3.4 45.7 - + + -
75B VAL* 3.9 1.7 - - - -
76B SER* 2.8 39.3 + - - -
77B HIS* 2.9 48.2 + + + +
79B VAL 5.1 0.8 - - - +
136B GLU* 4.8 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.9 4.0 - - - -
8B TYR* 1.3 94.5 - - - +
10B LYS* 1.3 69.4 + - - +
11B ARG* 3.4 1.4 + - - -
14B LEU* 3.8 34.3 - - + -
17B ALA* 4.0 17.0 - - - -
53B ASN* 2.9 26.8 + - + +
55B LEU* 4.0 26.2 - - - -
74B GLY 3.5 9.0 - - - +
75B VAL* 5.3 1.3 - - - -
76B SER* 3.9 3.4 - - - +
----------------------------------------------------------
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