Contacts of the helix formed by residues 129 - 141 (chain C) in PDB entry 1Z6T
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 ARG 129 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PHE* 5.2 1.4 - - - -
127C VAL* 3.7 9.1 + - + +
128C THR* 1.3 80.1 - - - +
130C LYS* 1.3 58.3 + - - +
131C LYS 3.4 1.8 - - - -
132C LEU* 3.3 21.1 + - + +
133C VAL* 3.0 34.3 + - + +
158C CYS 2.9 25.5 + - - -
159C GLY* 4.0 10.7 + - - -
163C LEU* 4.0 29.6 - - + +
282C VAL* 4.0 4.6 - - - +
283C GLU* 2.8 38.6 + - - -
286C LEU* 3.6 34.6 - - + +
290C LYS* 5.1 3.8 - - + +
321C PRO* 5.1 0.4 - - - +
902C ADP 3.9 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C THR* 3.7 32.4 - - + +
129C ARG* 1.3 71.7 - - - +
131C LYS* 1.3 61.5 + - - +
133C VAL* 4.5 4.7 - - - +
134C ASN* 2.8 46.6 + - - +
14D GLU* 5.2 14.2 + - - +
18D LYS* 4.6 13.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
129C ARG 3.4 0.6 - - - -
130C LYS* 1.3 78.8 - - - +
132C LEU* 1.3 66.1 + - + +
134C ASN* 4.0 4.6 - - - +
135C ALA* 3.1 25.5 + - + +
18D LYS* 4.3 23.7 - - - +
431D LYS* 3.7 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ARG* 3.3 34.2 + - + +
131C LYS* 1.3 83.6 - - + +
133C VAL* 1.3 62.4 + - - +
135C ALA* 3.3 6.0 + - + +
136C ILE* 3.1 30.1 + - + +
163C LEU* 3.9 21.5 - - + -
280C VAL* 4.1 14.5 - - + +
281C PRO 3.5 25.4 - - - +
282C VAL* 4.2 11.7 - - + -
283C GLU* 3.2 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PHE* 6.1 1.1 - - + -
129C ARG* 3.0 27.7 + - + +
130C LYS* 4.0 4.7 - - - +
132C LEU* 1.3 74.8 - - - +
134C ASN* 1.3 66.1 + - - +
136C ILE* 3.3 9.5 + - - +
137C GLN* 3.1 50.2 + - - +
163C LEU* 3.7 21.5 - - + +
166C GLU* 3.9 25.1 - - + +
167C ALA* 4.0 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LYS* 2.8 34.1 + - - +
131C LYS* 4.0 5.5 - - - +
133C VAL* 1.3 76.8 - - - +
135C ALA* 1.3 56.3 + - - +
137C GLN* 3.3 20.0 + - - +
138C GLN* 2.8 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LYS* 3.1 19.4 + - + +
132C LEU* 3.3 5.8 + - + +
134C ASN* 1.3 76.4 - - - +
136C ILE* 1.3 62.2 + - - +
138C GLN* 3.5 8.3 + - - +
139C LYS* 3.2 31.9 + - + +
280C VAL* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU 3.1 19.9 + - - +
133C VAL* 3.7 8.1 - - - +
134C ASN 3.3 0.2 - - - -
135C ALA* 1.3 75.9 - - - +
137C GLN* 1.3 58.5 + - - +
139C LYS* 3.2 5.3 + - - +
140C LEU* 2.9 31.3 + - + +
150C VAL* 4.5 2.0 - - + +
152C ILE* 3.8 25.8 - - + -
163C LEU* 4.0 31.9 - - + +
167C ALA* 3.6 19.7 - - + -
261C LEU* 4.1 26.7 - - + -
280C VAL* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C VAL* 3.1 26.8 + - - +
134C ASN* 3.5 25.8 + - - +
136C ILE* 1.3 72.1 - - - +
138C GLN* 1.3 62.2 + - + +
140C LEU* 3.4 9.8 + - - +
141C SER* 3.0 29.5 + - - -
166C GLU 4.0 2.4 + - - -
167C ALA* 2.8 39.9 + - + +
170C ASP* 3.6 27.3 - - - +
173C LEU* 3.8 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ASN* 2.8 24.5 + - + +
135C ALA* 3.7 9.0 - - - +
137C GLN* 1.3 77.2 - - - +
139C LYS* 1.3 63.3 + - + +
141C SER* 2.5 29.9 + - - -
142C LYS* 3.3 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ALA* 3.2 19.8 + - - +
136C ILE 3.5 5.4 - - - +
138C GLN* 1.3 76.0 - - + +
140C LEU* 1.3 67.5 + - - +
142C LYS* 2.9 40.8 + - - +
143C LEU* 3.7 4.3 + - - +
150C VAL* 3.8 23.0 - - + +
278C TYR* 3.8 34.7 - - + +
279C VAL 3.8 21.8 + - - +
280C VAL* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ILE* 2.9 36.4 + - + +
137C GLN* 3.7 6.1 - - - +
139C LYS* 1.3 77.9 - - - +
141C SER* 1.3 60.1 + - - +
143C LEU* 3.2 25.2 + - + +
144C LYS 4.5 1.0 + - - -
150C VAL* 4.0 20.0 - - + -
167C ALA* 4.4 8.1 - - + -
168C VAL* 4.4 11.4 - - + -
173C LEU* 4.2 24.2 - - + -
177C CYS* 4.8 2.5 - - - +
178C PHE* 4.1 22.1 - - + -
239C LEU* 3.9 30.3 - - + -
259C GLN* 5.2 0.2 - - - +
261C LEU* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLN 3.0 13.1 + - - -
138C GLN* 2.5 35.3 + - - -
140C LEU* 1.3 75.1 - - - +
142C LYS* 1.3 61.8 + - - +
143C LEU 3.3 0.4 - - - -
144C LYS* 3.5 29.1 + - - +
173C LEU* 4.6 2.6 - - - +
177C CYS* 4.1 22.3 - - - -
----------------------------------------------------------
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