Contacts of the strand formed by residues 94 - 100 (chain C) in PDB entry 3MX0
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 ILE 94 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 4.1 18.8 - - + -
88C ARG* 6.1 0.2 - - + -
91C ALA* 4.3 17.7 - - + -
93C ARG* 1.3 72.8 - - - +
95C PHE* 1.3 65.6 + - - +
96C ILE* 4.6 12.6 - - + +
123C TYR* 6.1 2.2 - - + -
142C ILE* 6.1 0.2 - - + -
169C SER* 3.1 5.4 - - - -
170C VAL* 2.9 45.9 + - + +
173C LEU* 3.3 28.7 - - + -
178C PHE* 4.3 17.3 - - + -
180C LEU* 5.1 4.0 - - + -
196C VAL* 3.9 24.2 - - + -
197C TYR 3.7 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ARG* 3.0 40.8 - - + -
94C ILE* 1.3 76.2 - - - +
96C ILE* 1.3 61.1 + - - +
97C GLU 4.3 0.4 - - - -
167C GLU* 4.1 17.5 - - - +
168C ARG 3.8 2.5 - - - -
169C SER* 3.2 24.0 - - - -
195C ARG 3.6 1.2 - - - +
196C VAL* 3.1 4.9 - - - +
197C TYR* 2.8 74.4 + + + +
198C TYR* 5.5 1.3 - - - -
199C LYS* 3.4 41.5 - - + -
249C VAL* 4.5 10.3 - - + -
250C ASP* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE* 4.6 11.9 - - + +
95C PHE* 1.3 77.1 - - - +
97C GLU* 1.3 60.3 + - - +
98C LEU* 3.5 29.9 + - + +
121C LEU* 4.3 15.7 - - + +
142C ILE* 4.1 21.3 - - + -
166C GLU 3.6 0.2 - - - +
167C GLU* 3.3 23.3 - - - +
168C ARG* 2.9 23.3 + - + +
169C SER* 5.4 2.0 - - - +
170C VAL* 5.9 0.2 - - + -
180C LEU* 3.9 41.7 - - + -
194C VAL* 4.4 4.3 - - + -
195C ARG 3.5 2.9 - - - -
196C VAL* 4.3 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PHE 4.3 0.4 - - - -
96C ILE* 1.3 70.9 - - - +
98C LEU* 1.3 60.7 + - - +
99C LYS* 3.3 31.5 + - + +
165C VAL* 3.9 20.9 - - + +
166C GLU 3.4 9.9 - - - +
167C GLU* 4.5 7.9 - - + +
193C SER* 3.1 21.5 + - - +
195C ARG* 2.7 59.8 + - + +
197C TYR* 4.9 10.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ILE* 3.7 20.9 - - + +
97C GLU* 1.3 69.5 - - - +
99C LYS* 1.3 68.3 - - - +
100C PHE* 4.3 6.7 - - + -
119C PHE* 4.8 4.5 - - + -
121C LEU* 3.2 33.4 - - + -
145C ILE* 4.4 20.4 - - + -
164C ASN 3.6 2.2 - - - +
166C GLU* 2.7 50.8 + - + +
167C GLU* 5.9 0.2 - - - -
168C ARG* 5.9 2.7 - - + -
182C PHE* 4.0 22.7 - - + -
191C LEU* 4.5 5.8 - - + -
193C SER 3.3 4.5 - - - +
194C VAL* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLU* 3.3 30.1 + - + +
98C LEU* 1.3 82.0 - - - +
100C PHE* 1.3 54.6 + - - +
163C LEU* 3.6 21.3 - - + -
164C ASN 3.6 4.0 - - - +
165C VAL* 4.1 25.6 - - + -
191C LEU* 3.5 1.9 - - - +
192C LEU* 2.6 37.3 + - + +
193C SER* 3.0 40.2 + - - +
195C ARG* 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 4.8 3.4 - - + -
99C LYS* 1.3 78.3 - - - +
101C THR* 1.3 59.2 + - - +
102C VAL* 5.2 4.9 - - + -
119C PHE* 3.0 46.9 - + + -
145C ILE* 3.9 12.3 - - + -
146C ALA* 4.3 5.2 - - - -
147C PRO* 4.3 11.2 - - + -
163C LEU* 3.1 13.8 - - - +
164C ASN* 2.8 71.6 + - + -
166C GLU* 3.7 21.5 - - + -
189C VAL* 3.7 8.7 - - + -
190C ALA 2.9 23.1 - - - +
191C LEU* 4.2 7.2 - - + +
----------------------------------------------------------
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