Contacts of the strand formed by residues 83 - 89 (chain A) in PDB entry 5ITX
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 GLY 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 5.8 1.4 - - - +
79A PHE* 3.0 42.3 + - - +
80A GLY 4.6 0.2 + - - -
81A MET 3.9 0.4 - - - -
82A SER* 1.3 78.1 - - - +
84A SER* 1.3 63.8 + - - -
114A PHE* 4.0 13.2 - - - -
115A VAL 3.4 5.8 - - - -
116A ASP* 3.6 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 4.0 5.2 - - - -
82A SER 4.5 2.1 + - - -
83A GLY* 1.3 74.4 - - - -
85A PHE* 1.3 67.8 + - - +
86A GLN* 4.3 9.6 + - - -
114A PHE* 3.4 12.1 - - - -
115A VAL* 2.8 49.6 + - - +
244A TYR* 3.4 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 4.7 2.2 - - + +
13A PHE* 3.6 12.4 - - + -
14A VAL* 4.1 19.1 - - + -
56A LEU* 3.8 28.7 - - + -
58A LEU* 4.2 19.5 - - + -
77A PHE* 3.8 34.1 - + - -
79A PHE* 3.8 27.4 - + - -
84A SER* 1.3 74.6 - - - +
86A GLN* 1.3 64.6 + - - +
101A PHE* 4.6 6.3 - + - -
112A LEU* 4.3 15.7 - - + -
113A CYS 3.3 14.1 - - - -
114A PHE* 3.7 21.5 - + + -
243A GLY 5.0 1.0 - - - +
244A TYR* 3.0 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 4.2 3.1 - - - -
84A SER* 4.2 8.5 + - - +
85A PHE* 1.3 77.3 - - - +
87A LEU* 1.3 60.1 + - - +
88A VAL* 3.8 23.2 - - + +
94A PRO* 3.8 14.9 - - + +
111A ALA 3.4 1.9 - - - +
112A LEU* 3.3 8.6 - - - +
113A CYS* 2.9 34.4 + - + +
115A VAL* 3.8 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 3.9 23.9 - - + -
17A ALA* 3.9 22.7 - - + +
18A CYS* 5.4 1.1 - - - -
21A LEU* 3.9 28.5 - - + -
23A PHE* 5.1 2.0 - - + -
86A GLN* 1.3 72.5 - - - +
88A VAL* 1.3 61.3 + - - +
89A PRO* 5.0 0.3 - - - +
110A LEU* 4.0 31.2 - - + -
111A ALA 3.6 4.5 - - - +
112A LEU* 3.6 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 3.8 31.2 - - + +
87A LEU* 1.3 79.0 - - - +
89A PRO* 1.3 78.6 - - + +
92A GLU 3.8 14.1 - - - +
93A LEU* 4.0 14.1 - - + -
94A PRO* 3.8 23.3 - - + -
110A LEU* 3.5 8.0 - - - +
111A ALA 2.7 46.2 + - - +
113A CYS* 4.3 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU 5.0 0.2 - - - +
88A VAL* 1.3 97.9 - - + +
90A ARG* 1.3 56.9 - - - +
91A GLU 3.1 2.7 - - - +
92A GLU* 2.9 57.2 + - + +
109A ARG 3.9 8.1 - - - +
110A LEU* 4.0 10.5 - - + -
----------------------------------------------------------
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