Contacts of the helix formed by residues 128 - 138 (chain C) in PDB entry 2XH2
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 PRO 128 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ASN 4.9 0.9 - - - +
127C VAL* 1.3 91.4 - - + +
129C LEU* 1.3 68.0 + - - +
130C TYR* 3.4 46.2 - - + +
131C LYS* 3.1 19.0 + - + +
132C HIS 3.2 8.3 + - - -
385C ASP* 5.1 0.7 - - - +
418C GLU* 3.7 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C SER* 3.8 36.1 - - - +
119C ARG* 4.2 24.2 - - + +
122C ALA* 4.0 10.6 - - + +
127C VAL 3.7 0.6 + - - -
128C PRO* 1.3 71.3 - - - +
130C TYR* 1.3 63.6 + - - +
132C HIS* 3.0 5.6 + - + +
133C LEU* 2.9 41.3 + - + +
381C THR 6.1 0.2 - - - -
382C PHE* 3.7 31.6 - - + +
385C ASP* 3.6 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C PRO* 3.4 24.3 - - + +
129C LEU* 1.3 75.0 - - - +
131C LYS* 1.3 68.1 + - + +
133C LEU* 3.3 1.6 + - - -
134C ALA* 2.9 25.3 + - - +
144C TYR* 3.7 22.9 - + - -
385C ASP* 3.1 52.8 + - - +
388C VAL* 4.0 15.7 - - + -
389C GLY* 3.3 9.9 - - - +
415C ILE* 3.7 28.3 - - + -
418C GLU* 2.6 38.4 + - - +
419C LEU* 3.6 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C VAL* 3.6 30.3 - - + -
128C PRO* 3.1 21.9 + - + +
130C TYR* 1.3 78.2 - - + +
132C HIS* 1.3 65.8 + - - +
134C ALA* 3.2 3.5 + - - +
135C ASP* 2.8 57.2 + - - +
141C THR* 4.8 15.1 + - + +
144C TYR* 3.3 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C VAL 4.9 0.2 + - - -
84C LYS 4.0 8.4 + - - -
86C GLN* 4.9 1.6 + - - -
118C SER* 3.3 30.8 + - - -
121C ALA* 3.3 24.1 - - + +
122C ALA* 3.8 20.9 - - + -
125C LYS* 3.0 34.6 + - + +
127C VAL* 3.9 9.3 - - + +
128C PRO 3.2 2.2 + - - -
129C LEU* 3.0 9.1 + - + +
131C LYS* 1.3 81.0 - - - +
133C LEU* 1.3 59.3 + - + +
135C ASP* 3.2 5.9 + - - +
136C LEU* 2.9 65.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C SER* 4.3 2.9 - - - +
129C LEU* 2.9 39.6 + - + +
130C TYR 3.8 4.0 - - - +
132C HIS* 1.3 74.3 - - + +
134C ALA* 1.3 62.2 + - - +
136C LEU* 3.4 13.8 + - + +
137C SER* 2.8 30.6 + - - -
352C LEU* 3.8 32.5 - - + -
356C ILE* 4.9 2.7 - - + +
382C PHE* 3.8 20.9 - - + -
385C ASP* 3.8 5.6 - - + +
386C LEU* 3.6 39.9 - - + +
389C GLY* 4.2 11.1 - - - -
390C LEU* 5.2 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C TYR 2.9 14.7 + - - +
131C LYS 3.2 9.8 + - - +
133C LEU* 1.3 74.1 - - - +
135C ASP* 1.3 60.2 + - - +
137C SER* 3.4 0.6 + - - -
138C LYS* 3.0 9.0 + - - -
139C SER* 2.9 32.3 + - - -
140C LYS 5.4 0.2 - - - +
141C THR* 3.7 29.2 - - + -
144C TYR* 4.2 5.8 - - + -
389C GLY* 3.4 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LYS* 3.0 32.0 + - - +
127C VAL* 5.2 0.3 - - - +
131C LYS* 2.8 54.1 + - - +
132C HIS* 3.2 8.6 + - - +
134C ALA* 1.3 75.6 - - - +
136C LEU* 1.3 65.2 + - + +
138C LYS* 3.2 20.0 + - - +
141C THR* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LYS 3.8 15.3 - - - +
86C GLN* 3.7 31.4 - - + +
87C LYS* 5.8 3.8 - - - -
125C LYS* 5.7 0.2 - - - +
132C HIS* 2.9 53.0 + - + +
133C LEU* 3.8 10.8 - - + +
134C ALA 3.3 0.2 - - - -
135C ASP* 1.3 76.9 - - + +
137C SER* 1.3 59.0 + - - +
138C LYS* 3.7 10.4 + - - +
352C LEU* 4.0 23.1 - - + -
356C ILE* 3.9 19.0 - - + +
360C GLN* 4.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU 2.8 20.5 + - - -
134C ALA 3.4 2.9 + - - -
136C LEU* 1.3 76.9 - - - +
138C LYS* 1.3 66.5 + - - +
139C SER* 2.7 25.5 + - - -
356C ILE* 3.8 12.6 - - - -
360C GLN* 3.0 28.5 + - - +
389C GLY 3.6 5.9 + - - -
390C LEU* 3.6 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LYS* 4.7 14.8 - - - +
134C ALA 3.0 6.3 + - - -
135C ASP* 3.2 18.2 + - - +
136C LEU 3.4 7.5 + - - +
137C SER* 1.3 81.6 - - - +
139C SER* 1.3 61.4 + - - +
140C LYS 4.1 0.5 + - - -
360C GLN* 4.8 5.5 - - - +
----------------------------------------------------------
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