Contacts of the helix formed by residues 131 - 143 (chain C) in PDB entry 4HYY
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 GLY 131 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ARG 4.8 0.2 - - - -
130C THR* 1.3 78.9 - - - +
132C LYS* 1.3 53.8 + - - +
133C THR 3.3 2.7 - - - -
134C GLN* 3.5 19.9 - - - +
135C LEU* 2.7 38.7 + - - +
303C LEU* 4.3 7.2 - - - -
311C ARG* 3.8 7.2 - - - +
328C PHE* 4.9 4.5 - - - -
330C ILE* 4.6 10.3 - - - -
335C ILE* 4.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ALA* 3.9 21.3 - - + +
126C GLY* 3.0 32.1 + - - +
127C GLU 4.1 12.3 + - - -
128C PHE* 5.0 6.4 + - - +
130C THR* 2.6 15.6 + - - +
131C GLY* 1.3 73.8 - - - +
133C THR* 1.3 60.7 + - - +
135C LEU* 3.2 5.7 + - - +
136C SER* 3.0 25.3 + - - -
223C ASP* 5.4 1.6 - - - +
265C PHE* 4.3 0.5 - - - -
267C THR* 3.7 25.2 - - + +
268C ASN 3.3 25.5 + - - +
269C GLN* 4.5 14.0 - - - +
303C LEU* 3.9 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C THR 4.3 1.8 + - - -
131C GLY 3.3 0.2 - - - -
132C LYS* 1.3 77.7 - - - +
134C GLN* 1.3 75.3 + - - +
135C LEU 3.1 1.3 - - - -
136C SER* 3.1 3.0 + - - -
137C HIS* 3.0 51.7 + - + -
162C GLU* 6.0 0.2 - - - +
164C THR* 3.9 20.2 + - - +
223C ASP* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C THR 5.6 0.2 - - - +
131C GLY* 3.1 15.6 + - - +
133C THR* 1.3 85.4 - - - +
135C LEU* 1.3 58.0 + - - +
137C HIS* 3.6 3.6 + - - +
138C THR* 2.9 31.2 + - - -
169C ARG* 2.9 42.7 + - - +
173C ILE* 5.1 0.2 - - - +
330C ILE* 4.2 21.3 - - + +
331C THR 4.8 5.3 + - - -
334C GLY* 4.8 4.7 - - - -
335C ILE* 3.9 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C THR* 4.3 22.7 - - + +
108C PHE* 3.9 28.3 - - + -
116C ILE* 5.4 2.5 - - + -
124C ALA* 4.6 8.5 - - + -
131C GLY 2.7 20.5 + - - +
132C LYS 3.5 4.5 - - - +
134C GLN* 1.3 71.3 - - - +
136C SER* 1.3 66.9 + - - +
138C THR* 5.0 0.4 - - - -
139C LEU* 3.0 56.0 + - + +
265C PHE* 3.6 26.0 - - + -
301C ILE* 6.3 0.4 - - + -
303C LEU* 5.0 6.3 - - + -
328C PHE* 6.0 0.7 - - + -
335C ILE* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LYS 3.0 14.3 + - - -
133C THR* 3.1 12.1 + - - -
135C LEU* 1.3 78.7 - - - +
137C HIS* 1.3 65.0 + - - +
139C LEU* 3.3 5.6 + - - +
140C CYS* 3.3 21.1 + - - -
158C PHE* 4.0 25.8 - - - -
221C ILE* 3.7 11.5 - - - +
223C ASP* 3.9 8.2 + - - -
265C PHE* 3.6 21.1 - - - -
267C THR* 3.8 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C THR* 3.0 50.8 + - + +
134C GLN* 4.1 4.2 + - - +
136C SER* 1.3 77.3 - - - +
138C THR* 1.3 68.3 + - - +
140C CYS* 3.0 15.5 + - - +
141C VAL* 3.8 1.7 + - - +
158C PHE* 5.3 2.2 - + - -
164C THR 3.6 13.2 + - - -
165C PHE* 3.5 20.7 - + - -
166C ARG* 3.0 43.3 + - - +
169C ARG* 3.7 23.1 + - + +
170C LEU* 3.2 32.3 - - + +
173C ILE* 4.2 8.7 - - + -
223C ASP* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C THR 3.3 26.9 - - - +
104C GLY* 4.6 0.9 - - - +
134C GLN 2.9 18.8 + - - -
135C LEU* 3.8 4.7 - - + -
136C SER 3.3 0.2 - - - -
137C HIS* 1.3 77.2 - - - +
139C LEU* 1.3 58.6 + - - +
141C VAL* 3.0 20.1 + - - +
142C THR* 3.0 26.2 + - + +
173C ILE* 4.1 16.3 - - + +
176C ARG* 4.9 0.2 - - - +
177C PHE* 4.9 1.8 - - + -
334C GLY* 3.2 8.7 - - - -
335C ILE* 2.8 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ILE* 3.8 15.7 - - + -
102C THR 3.6 22.4 - - - +
103C THR* 4.5 2.2 - - - -
116C ILE* 4.0 19.5 - - + -
135C LEU* 3.0 38.5 + - + +
136C SER* 3.6 4.9 - - - +
137C HIS 3.1 0.2 - - - -
138C THR* 1.3 78.8 - - - +
140C CYS* 1.3 60.6 + - - +
141C VAL 3.1 0.4 - - - -
142C THR* 3.5 3.8 - - - -
143C ALA* 3.1 28.8 + - - +
219C LEU* 3.6 18.1 - - + +
221C ILE* 4.3 1.8 - - + -
265C PHE* 3.6 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C SER 3.3 15.7 + - - -
137C HIS* 3.0 12.7 + - - +
139C LEU* 1.3 75.2 - - - +
141C VAL* 1.3 53.7 + - - +
144C GLN* 2.7 33.3 + - - +
156C ILE* 3.5 17.0 - - - +
158C PHE* 3.7 28.0 - - - -
165C PHE* 4.1 14.8 - - - -
170C LEU* 3.7 18.2 - - + -
184C VAL* 4.4 0.4 - - - +
188C VAL* 4.1 14.4 - - + -
221C ILE* 3.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C HIS 4.2 7.0 - - - +
138C THR 3.0 5.9 + - - +
140C CYS* 1.3 81.4 - - - +
142C THR* 1.3 58.3 + - - +
143C ALA 3.1 1.3 - - - -
144C GLN* 2.7 34.3 + - - +
145C LEU* 3.7 9.0 - - + +
170C LEU* 4.2 13.2 - - + +
173C ILE* 3.9 29.2 - - + +
174C ALA* 4.5 4.0 - - - +
177C PHE* 4.2 28.5 - - + -
179C VAL* 5.0 1.3 - - + -
184C VAL* 3.8 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ILE* 3.6 6.1 - - - +
102C THR* 2.8 46.8 + - + +
104C GLY 4.3 3.6 - - - +
138C THR* 3.0 17.5 + - + +
139C LEU* 3.5 15.2 - - - -
141C VAL* 1.3 78.0 - - - +
143C ALA* 1.3 58.4 + - - +
145C LEU* 2.9 34.8 + - + +
151C TYR* 4.7 1.7 - - - -
177C PHE* 3.7 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ILE* 3.8 21.5 - - + +
139C LEU 3.1 17.1 + - - +
142C THR* 1.3 80.9 + - - +
144C GLN* 1.3 58.4 + - - +
145C LEU 3.4 0.2 + - - -
151C TYR* 2.9 21.7 + - - +
153C GLY* 3.3 2.6 - - - -
154C GLY 3.0 15.4 + - - +
155C LYS 5.3 0.9 - - - +
156C ILE* 3.8 23.6 - - + -
218C LYS* 5.3 1.1 - - + -
219C LEU* 3.8 13.2 - - + -
----------------------------------------------------------
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