Contacts of the strand formed by residues 88 - 93 (chain C) in PDB entry 1I3R
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 GLU 88 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA 6.0 0.2 - - - +
87C PRO* 1.3 74.6 - - - +
89C VAL* 1.3 62.9 + - - +
90C THR* 5.3 2.2 - - - +
108C PHE 3.6 1.3 - - - +
109C ILE* 3.6 1.6 - - - -
110C ASP* 2.9 39.8 + - + +
111C LYS* 3.3 42.7 + - + +
174C LEU* 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PRO* 4.1 6.7 + - + +
88C GLU* 1.3 81.5 - - - +
90C THR* 1.3 72.0 + - - +
107C CYS* 3.8 27.6 - - - -
108C PHE 3.4 4.7 - - - +
109C ILE* 4.7 3.6 - - + -
163C CYS* 4.7 2.7 - - - +
165C VAL* 4.0 31.6 - - + -
174C LEU* 3.4 25.7 - - + +
176C LYS* 3.4 42.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C GLU* 5.3 2.3 - - - +
89C VAL* 1.3 79.5 + - - +
91C VAL* 1.3 74.6 + - - +
92C LEU* 4.2 12.8 + - + +
106C ILE 3.4 1.2 - - - +
107C CYS 3.4 0.5 - - - -
108C PHE* 2.6 56.5 + - + +
176C LYS* 5.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C THR* 1.3 80.6 - - - +
92C LEU* 1.3 64.4 + - - +
105C LEU* 4.3 9.6 - - + -
106C ILE 3.1 9.4 - - - +
107C CYS* 4.2 4.5 - - - -
121C TRP* 4.3 16.8 - - + -
161C TYR* 6.0 0.2 - - + -
162C ASP* 6.2 0.9 - - - -
163C CYS* 3.7 29.6 - - + +
176C LYS* 3.7 27.2 - - + +
177C HIS 5.0 3.1 - - - +
178C TRP* 3.8 38.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C THR* 4.3 17.3 - - + +
91C VAL* 1.3 78.0 - - - +
93C SER* 1.3 60.9 + - - +
105C LEU* 3.6 7.0 - - - +
106C ILE* 2.6 72.5 + - + +
108C PHE* 4.9 6.1 - - + -
178C TRP* 4.5 6.3 - - - +
174D VAL* 3.9 26.0 - - + -
176D ASN* 4.8 0.7 - - - +
182D GLN* 3.7 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 1.3 79.0 - - - +
94C ARG* 1.3 61.7 + - - +
95C SER 2.8 26.0 + - - -
96C PRO* 4.8 0.3 - - - +
97C VAL* 3.4 24.2 + - - +
103C ASN* 4.4 4.5 - - - -
104C ILE 3.5 7.9 - - - -
105C LEU* 4.4 2.4 - - - +
106C ILE* 4.5 0.4 - - - -
153C PHE* 4.7 4.3 - - - -
178C TRP* 4.6 12.4 - - - +
182D GLN* 2.8 24.5 + - - +
----------------------------------------------------------
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