Contacts of the strand formed by residues 98 - 102 (chain C) in PDB entry 2O2C
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 PHE 98 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B MET* 3.9 15.3 - - - -
604B LEU* 3.4 26.2 - - + -
88C LYS* 3.8 28.9 - - + -
89C VAL 3.3 14.6 - - - +
90C SER* 4.3 2.5 - - - -
91C LEU* 3.7 9.5 - - - +
96C GLU 3.6 15.5 - - - +
97C ASN* 1.3 80.1 + - - +
99C LEU* 1.3 62.4 + - - +
100C PHE* 3.9 18.4 - - + -
463C ILE* 3.7 26.5 - - + -
530C LEU 3.6 23.8 - - - -
531C ILE* 3.3 30.4 - - - +
532C LYS* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C VAL 3.8 2.1 - - - +
88C LYS* 3.7 0.5 - - - -
89C VAL* 2.9 41.1 + - + +
91C LEU* 4.3 9.6 - - + -
98C PHE* 1.3 74.4 - - - +
100C PHE* 1.3 60.0 + - - +
101C LEU 4.1 0.2 + - - -
356C ILE* 4.0 17.9 - - + -
369C VAL* 5.1 8.5 - - + +
529C LEU* 3.9 29.6 - - + -
530C LEU 3.8 1.1 - - - +
531C ILE* 3.9 19.1 - - + -
541C ALA* 4.0 29.6 - - + +
542C ILE* 4.4 11.9 - - + +
545C MET* 4.0 21.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
596B GLY 5.8 3.4 - - - -
597B LEU* 3.8 33.0 - - + -
600B MET* 3.7 34.8 - - + -
82C GLY 5.1 0.7 - - - -
83C GLN* 6.3 1.1 - - - -
86C SER* 3.6 34.3 - - - -
87C VAL 3.5 16.6 - - - -
88C LYS* 3.8 14.4 - - + +
98C PHE* 3.9 15.7 - - + -
99C LEU* 1.3 73.1 - - - +
101C LEU* 1.3 60.0 + - - +
102C ASP* 4.0 14.6 - - + -
528C THR 3.4 2.5 - - - +
529C LEU* 3.2 8.6 - - - +
530C LEU* 2.8 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C SER* 3.2 6.5 - - - -
87C VAL* 3.0 33.8 + - + +
99C LEU* 4.1 1.4 + - + -
100C PHE* 1.3 73.0 - - - +
102C ASP* 1.3 73.3 + - - +
103C TYR* 4.0 24.0 - - + -
369C VAL* 3.8 50.7 - - + +
372C LEU* 4.5 2.9 - - + -
373C LEU* 4.0 34.3 - - + +
527C ASN* 4.2 10.8 - - + -
528C THR 3.6 2.9 - - - +
529C LEU* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B SER* 2.7 31.3 + - - +
597B LEU* 3.9 12.6 - - + +
82C GLY 4.4 5.2 - - - +
85C TYR 3.9 3.1 - - - +
86C SER* 4.0 8.5 - - - -
100C PHE* 4.0 17.6 + - + -
101C LEU* 1.3 73.8 - - - +
103C TYR* 1.3 58.0 - - - +
104C SER* 2.6 29.3 + - - -
105C LYS* 4.3 2.2 + - - +
526C SER 4.3 1.2 - - - +
527C ASN* 3.4 4.7 - - - -
528C THR* 2.8 48.3 + - - +
----------------------------------------------------------
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