Contacts of the strand formed by residues 77 - 82 (chain H) in PDB entry 3INU
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 77 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H CYS 3.2 10.7 + - - -
23H ALA* 4.1 9.0 - - - +
29H LEU* 3.2 12.8 - - - +
71H ARG* 3.6 0.5 - - - -
72H ASP 2.7 34.2 + - - -
75H GLU* 3.3 21.4 + - - +
76H ASN* 1.3 75.3 + - - +
78H LEU* 1.3 60.3 + - - +
79H TYR* 3.4 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H SER* 3.3 3.5 - - - -
22H CYS* 2.8 39.5 + - + +
29H LEU* 4.5 7.2 - - + -
34H MET* 3.7 21.3 - - + -
35H ASN 3.8 11.2 - - - +
36H TRP* 3.4 21.8 - - + +
51H ILE* 3.6 29.8 - - + -
69H ILE* 4.0 8.5 - - + -
70H SER 3.5 17.3 - - - +
71H ARG* 4.7 3.4 - - + -
77H SER* 1.3 75.8 - - - +
79H TYR* 1.3 64.8 + - - +
92H CYS* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ARG* 3.7 39.9 - - - +
20H LEU 3.4 4.0 - - - +
21H SER* 3.3 34.5 - - - -
36H TRP* 3.4 12.3 + - - -
68H THR 4.5 0.2 - - - -
69H ILE* 3.4 2.9 - - - +
70H SER* 2.7 57.3 + - - +
71H ARG 4.6 1.8 - - - -
72H ASP* 4.0 20.3 + - + +
75H GLU* 5.0 5.4 - - - +
77H SER* 3.4 32.8 + - - -
78H LEU* 1.3 76.1 - - - +
80H LEU* 1.3 61.5 + - - +
81H GLN 4.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H LEU 4.0 0.3 - - - +
19H ARG* 3.4 4.0 - - - -
20H LEU* 2.8 43.4 + - + -
36H TRP* 3.5 49.9 - - + +
48H VAL* 4.3 7.0 - - + -
49H SER* 4.6 6.7 - - - -
67H PHE* 4.0 30.3 - - + -
68H THR 3.6 6.3 - - - +
69H ILE* 3.8 23.6 - - + +
79H TYR* 1.3 73.0 - - - +
81H GLN* 1.3 59.4 + - - +
82H MET* 3.7 17.2 + - + +
90H TYR* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H SER* 4.2 8.1 + - - -
18H LEU 3.8 15.8 + - - +
19H ARG* 3.3 40.1 + - - +
66H ARG 3.7 2.3 - - - +
67H PHE* 3.3 4.6 - - - -
68H THR* 2.8 54.4 + - + +
79H TYR* 4.2 0.6 - - - +
80H LEU* 1.3 72.0 - - - +
82H MET* 1.3 94.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H SER* 3.0 7.3 - - - -
18H LEU* 2.8 56.5 + - + +
20H LEU* 3.5 38.1 - - + -
66H ARG 3.9 2.2 - - - -
67H PHE* 3.8 36.6 - - + -
80H LEU* 4.1 12.1 - - + +
81H GLN* 1.3 74.7 + - - +
82H ASN* 1.3 81.0 + - - +
90H TYR* 4.0 19.7 - - - -
109H VAL* 3.9 19.7 - - + -
----------------------------------------------------------
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