Contacts of the helix formed by residues 133 - 142 (chain A) in PDB entry 4JUY
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 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 3.6 26.7 - - - +
75A LEU* 3.8 15.2 - - - +
131A VAL 3.5 0.2 + - - -
132A GLN* 1.3 73.1 - - - +
134A GLY* 1.3 62.8 + - - +
135A ARG 3.3 2.9 - - - +
136A ASP* 3.2 12.1 + - - +
137A VAL* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.3 1.0 - - - +
98A LEU* 3.9 12.4 - - - +
128A VAL* 3.7 40.3 - - - +
131A VAL* 3.2 13.2 + - - +
132A GLN 3.3 1.0 + - - -
133A GLY* 1.3 77.2 - - - +
135A ARG* 1.3 61.8 + - - +
137A VAL* 3.2 13.3 + - - +
138A LEU* 3.4 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.4 52.6 - - - +
124A PHE* 4.1 11.0 - - + -
128A VAL* 4.5 0.2 - - - +
129A ASP* 2.9 41.1 + - - +
133A GLY 3.3 1.0 - - - +
134A GLY* 1.3 72.8 - - - +
136A ASP* 1.3 66.1 + - - +
138A LEU* 3.1 10.1 + - - +
139A ARG* 2.9 47.3 + - - +
146A GLU* 4.9 7.7 + - - -
151A LEU* 4.0 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 3.3 27.1 + - - -
133A GLY* 3.2 11.7 + - - +
135A ARG* 1.3 76.0 - - - +
137A VAL* 1.3 63.8 + - + +
139A ARG* 2.7 33.9 + - - +
140A LEU* 2.9 28.6 + - + +
204A UNX 3.7 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.7 22.0 - - + -
75A LEU* 4.4 9.4 - - + -
95A LEU* 6.0 0.2 - - + -
98A LEU* 3.9 28.9 - - + -
133A GLY 3.2 16.8 - - - +
134A GLY 3.6 5.6 - - - +
135A ARG 3.1 0.6 - - - -
136A ASP* 1.3 75.9 - - + +
138A LEU* 1.3 66.6 + - - +
140A LEU* 3.0 19.4 + - + +
141A TYR* 3.2 18.0 + - + -
168A VAL* 4.0 11.9 - - + -
172A VAL* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.0 10.8 - - + -
101A TYR* 4.0 37.0 - - + -
117A VAL* 4.1 20.6 - - + -
119A PHE* 6.3 0.2 - - + -
124A PHE* 3.5 33.2 - - + -
128A VAL* 4.9 0.7 - - + -
134A GLY 3.4 9.6 + - - +
135A ARG* 3.1 8.3 + - - +
137A VAL* 1.3 78.9 - - - +
139A ARG* 1.3 64.0 + - - +
141A TYR* 3.0 15.4 + - + +
142A GLY 3.4 0.7 + - - -
143A TYR* 3.2 39.8 + - + -
151A LEU* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 2.9 45.7 + - - +
136A ASP* 2.7 42.2 + - - +
138A LEU* 1.3 77.4 - - - +
140A LEU* 1.3 57.1 + - + +
142A GLY* 3.0 20.4 + - - -
143A TYR 3.6 19.5 + - - +
144A THR* 3.6 25.3 + - + +
146A GLU* 2.7 30.1 + - - +
151A LEU* 4.0 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 3.8 44.4 - - + +
70A LEU* 4.2 17.3 - - + +
71A ASP 5.1 1.3 - - - +
136A ASP* 2.9 21.4 + - + +
137A VAL* 3.0 17.7 + - + +
139A ARG* 1.3 76.0 - - + +
141A TYR* 1.3 60.4 + - - +
142A GLY 3.5 0.2 + - - -
164A GLN* 2.9 33.6 + - - +
168A VAL* 3.8 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 2.6 36.0 + - + -
99A GLU* 3.9 1.2 + - - -
101A TYR* 4.1 7.4 - - + -
102A GLY* 3.5 20.6 + - - -
105A LEU* 3.7 16.4 - - + -
137A VAL* 3.2 20.9 + - + -
138A LEU* 3.0 24.7 + - + +
140A LEU* 1.3 77.1 - - - +
142A GLY* 1.3 56.4 + - - +
143A TYR* 4.2 4.0 - + + -
153A PHE* 3.4 15.4 - - - -
160A PRO* 5.0 0.2 - - - +
161A ASP* 5.1 2.1 + - - +
164A GLN* 5.1 3.2 - - - +
165A VAL* 3.5 31.4 - - + +
168A VAL* 3.4 30.5 - - + -
169A THR* 3.3 25.1 + - - -
172A VAL* 3.7 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG 3.0 9.8 + - - -
140A LEU 3.2 0.8 - - - -
141A TYR* 1.3 80.4 - - - +
143A TYR* 1.3 56.9 + - - +
144A THR* 2.8 25.6 + - - -
153A PHE* 3.6 34.7 - - - -
154A PRO* 3.8 2.3 - - - +
157A GLN* 5.5 2.7 - - - -
----------------------------------------------------------
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