Contacts of the strand formed by residues 71 - 75 (chain I) in PDB entry 3CII
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 ASN 71 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I CYS* 3.9 1.8 - - - -
66I VAL 3.7 0.3 - - - +
67I GLY* 3.3 6.4 - - - -
68I TYR 2.8 30.6 + - - +
69I ARG* 3.4 12.7 + - - +
70I CYS* 1.3 86.0 - - - +
72I CYS* 1.3 63.7 + - - +
73I TYR* 3.1 35.0 + - + -
100I GLN* 6.3 0.4 - - - +
104I GLU* 4.5 3.0 + - - +
175I LYS* 3.6 22.3 - - + +
176I GLN 4.6 6.3 - - - +
177I GLN* 4.4 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 72 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I SER 3.8 6.5 - - - -
61I CYS* 2.0 57.4 - - - -
62I GLN* 4.1 3.6 - - - -
65I TRP* 3.9 13.5 - - + -
66I VAL 3.6 0.2 - - - -
70I CYS 4.5 0.2 + - - -
71I ASN* 1.3 72.8 - - - +
73I TYR* 1.3 59.9 + - - +
175I LYS* 3.4 5.2 - - - -
176I GLN* 2.9 65.9 + - + +
177I GLN 4.6 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I TRP* 3.4 10.9 - - - -
66I VAL* 2.7 57.0 + - + +
68I TYR* 3.9 33.2 + + + -
69I ARG* 4.9 3.8 - - - +
71I ASN* 3.1 31.9 + - + -
72I CYS* 1.3 74.2 - - - +
74I PHE* 1.3 59.5 + - - +
75I ILE* 5.0 2.7 - - + -
97I LEU* 4.8 2.0 - - + -
104I GLU* 3.2 31.2 + - + +
105I LEU* 4.5 11.7 - - + -
107I PHE* 4.2 17.9 - + + -
108I MET* 6.2 0.4 - - + -
173I ILE* 4.6 11.7 - - + -
174I CYS 3.5 11.0 - - - +
175I LYS* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I LYS* 3.7 44.0 - - + -
65I TRP* 3.2 39.2 - + + -
73I TYR* 1.3 70.3 - - - +
75I ILE* 1.3 75.0 + - - +
76I SER* 3.9 2.2 + - - -
77I SER* 5.1 8.7 - - - -
78I GLU* 5.3 3.6 - - - -
92I GLN* 3.9 24.0 - - - -
172I TYR* 3.8 24.1 - + - +
173I ILE* 3.1 7.9 - - - -
174I CYS* 2.9 49.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I LYS 5.5 1.0 + - - +
66I VAL* 3.8 26.7 - - + -
73I TYR* 4.2 3.6 + - + -
74I PHE* 1.3 92.0 - - - +
76I SER* 1.3 67.8 + - - +
77I SER* 3.9 1.6 + - - -
107I PHE* 4.2 2.0 - - + -
108I MET* 3.9 29.2 - - + -
115I TYR* 3.4 37.2 - - + +
172I TYR 4.1 2.7 - - - -
173I ILE* 4.4 7.2 - - + -
165J PHE* 5.3 5.2 - - + -
168J ILE* 4.3 13.0 - - + -
169J ILE* 4.2 20.2 - - + -
----------------------------------------------------------
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