Contacts of the helix formed by residues 96 - 104 (chain C) in PDB entry 5X11
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 ASP 96 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C VAL 3.4 2.8 + - - +
95C LYS* 1.3 73.8 - - - +
97C GLU* 1.3 63.0 + - - +
98C PHE* 3.1 15.9 + - - +
99C MET* 3.0 32.7 + - + +
100C LEU* 3.3 9.2 + - - +
124C ARG* 4.9 5.1 + - - -
168C TYR* 2.5 42.3 + - - -
33D PHE* 3.0 26.2 + - + +
34D TRP* 4.5 1.1 - - - -
160D LYS* 4.8 1.2 - - - -
164D ARG* 5.5 0.9 - - - +
----------------------------------------------------------
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 LYS 4.2 0.4 - - - -
96C ASP* 1.3 73.4 + - - +
98C PHE* 1.3 62.4 + - - +
100C LEU* 3.3 20.5 - - - +
101C LYS* 3.5 11.5 + - - +
3D VAL* 3.6 39.9 - - + +
34D TRP* 4.2 16.4 - - + -
83D TRP* 3.2 28.6 + - + -
88D GLN* 3.5 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASP* 3.1 11.4 + - - +
97C GLU* 1.3 80.4 - - - +
99C MET* 1.3 63.2 + - - +
101C LYS* 3.1 16.4 + - + +
102C ALA* 3.1 21.3 + - + -
116C LEU* 4.0 33.2 - - + -
117C PHE* 4.0 24.2 - + - -
120C GLN* 3.4 39.9 - - + +
124C ARG* 5.8 0.2 - - - +
168C TYR* 3.5 18.2 - - - +
171C TRP* 3.9 15.0 - + - -
172C LEU* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASP* 3.0 27.3 + - - +
98C PHE* 1.3 83.8 - - - +
100C LEU* 1.3 63.6 + - - +
102C ALA* 3.2 15.9 + - + +
103C TYR* 3.1 22.2 + - - +
168C TYR* 4.4 0.2 - - - -
171C TRP* 3.6 28.5 - - + -
33D PHE* 3.5 38.4 - - + -
156D LEU 3.6 13.2 - - - +
157D VAL* 3.8 19.0 - - - +
160D LYS* 3.5 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASP 3.3 6.7 + - - +
97C GLU* 3.3 12.8 - - + +
99C MET* 1.3 77.7 - - - +
101C LYS* 1.3 61.8 + - - +
103C TYR* 3.2 13.6 + - - +
104C PHE* 3.2 36.9 + - + -
3D VAL* 3.5 31.6 - - + +
7D ALA* 4.1 21.1 - - + -
30D LEU* 3.6 37.5 - - + -
33D PHE* 5.0 1.9 - - - +
34D TRP* 3.9 24.9 - - + -
83D TRP* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLU* 3.5 9.8 + - - +
98C PHE* 3.1 17.3 + - + +
100C LEU* 1.3 75.9 - - - +
102C ALA* 1.3 65.3 + - - +
104C PHE* 3.0 12.8 + - - +
105C ILE* 3.4 10.6 + - - +
108C LEU* 5.4 1.9 - - - +
116C LEU* 3.9 25.2 - - + +
117C PHE* 5.8 0.3 - - - -
83D TRP* 2.8 44.5 + - + -
84D LEU* 3.1 37.3 + - + +
86D ARG 2.7 30.1 + - - -
88D GLN* 2.8 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 3.1 12.2 + - + +
99C MET* 3.2 34.1 + - + +
101C LYS* 1.3 75.3 - - - +
103C TYR* 1.3 62.4 + - - +
105C ILE* 3.3 25.6 - - - +
117C PHE* 4.2 19.9 - - + -
171C TRP* 4.5 2.0 - - + -
153D GLY* 3.6 2.7 - - - -
156D LEU* 3.4 24.2 - - + +
157D VAL* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C MET 3.1 12.1 + - - +
100C LEU 3.4 9.6 - - - +
101C LYS 3.1 0.2 - - - -
102C ALA* 1.3 76.7 - - - +
104C PHE* 1.3 77.5 - + - +
105C ILE* 3.3 2.9 + - - +
106C SER 5.2 0.2 + - - -
11D LEU* 3.9 22.4 - - + -
13D ARG* 3.5 24.0 + - - -
25D TYR* 3.7 23.0 - - - -
29D GLU* 3.0 35.4 + - + -
30D LEU* 3.6 28.1 - - + +
153D GLY* 3.8 22.4 - - - -
154D HIS* 4.1 13.7 - - + -
157D VAL* 3.7 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C LEU* 3.2 39.7 + - + -
101C LYS 3.0 9.7 + - - +
103C TYR* 1.3 101.6 - + - +
105C ILE* 1.3 57.1 + - - +
106C SER 3.2 2.9 - - - -
107C SER* 3.0 28.3 + - - -
6D TYR 3.8 7.6 - - - -
7D ALA* 3.2 25.6 - - - -
10D GLY* 3.2 40.2 - - - -
11D LEU* 3.4 12.1 - - + -
13D ARG* 3.5 23.4 - - - +
30D LEU* 4.6 0.7 - - + -
80D LEU* 4.8 0.7 - - + -
83D TRP* 4.3 14.4 - + - -
84D LEU* 4.2 16.9 - - + +
----------------------------------------------------------
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