Contacts of the helix formed by residues 119 - 132 (chain B) in PDB entry 3PL7
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 ALA 119 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLY 3.4 3.7 + - - +
118B THR* 1.3 75.6 + - - +
120B TYR* 1.3 63.4 + - - +
121B GLN* 3.4 7.4 - - + +
122B SER* 2.9 22.5 + - - +
123B PHE 3.8 2.4 + - - -
169B TRP* 3.7 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 1.3 74.5 - - - +
121B GLN* 1.3 66.8 + - + +
123B PHE* 3.0 13.7 + + - +
124B GLU* 2.8 75.9 + - + +
169B TRP* 3.6 61.6 - + + +
172B THR* 3.7 22.5 + - + +
173B TYR* 3.6 20.9 - - + -
176B ASP* 4.8 2.9 + - - -
177B HIS* 4.1 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 3.4 5.4 - - + +
120B TYR* 1.3 86.8 - - - +
122B SER* 1.3 55.9 + - - +
124B GLU* 3.0 27.7 + - - +
125B GLN* 3.0 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 6.2 0.2 - - - +
118B THR* 3.7 20.1 + - - -
119B ALA* 2.9 25.6 + - - +
121B GLN* 1.3 78.4 - - - +
123B PHE* 1.3 66.2 + - - +
125B GLN* 3.3 14.7 + - - +
126B VAL* 3.2 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 5.8 0.4 - - - +
119B ALA 4.3 0.9 - - - +
120B TYR* 3.0 11.8 + + - +
122B SER* 1.3 79.0 + - - +
124B GLU* 1.3 70.6 + - - +
126B VAL* 3.0 17.0 + - - +
127B VAL* 3.0 39.2 + - + +
143B PHE* 4.2 7.2 - + - -
146B PHE* 3.8 23.8 - + - -
147B GLY* 5.3 0.9 - - - -
150B LEU* 4.1 13.7 - - + -
166B ILE* 5.1 3.4 - - + -
169B TRP* 3.7 61.5 - + + -
170B MET* 4.1 25.4 - - + -
173B TYR* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TYR* 2.8 50.4 + - + +
121B GLN* 3.0 34.8 + - - +
123B PHE* 1.3 79.0 - - - +
125B GLN* 1.3 53.8 + - - +
127B VAL* 3.4 0.7 + - - +
128B ASN* 2.7 58.7 + - - +
173B TYR* 3.9 14.4 - - + -
177B HIS* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLN* 3.0 23.7 + - + +
122B SER* 3.5 13.0 - - - +
123B PHE 3.2 0.4 - - - -
124B GLU* 1.3 77.2 + - - +
126B VAL* 1.3 62.5 + - + +
128B ASN* 3.8 18.0 - - - +
129B GLU* 4.0 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 6.0 1.8 - - + -
112B LEU* 4.4 28.0 - - + -
122B SER 3.2 12.9 + - - +
123B PHE* 3.0 11.8 + - - +
125B GLN* 1.3 77.4 - - + +
127B VAL* 1.3 62.0 + - - +
128B ASN 3.0 0.9 - - - -
129B GLU* 2.8 29.0 + - - +
130B LEU* 3.7 2.6 + - - +
146B PHE* 4.0 27.8 - - + -
79C MET* 4.5 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PHE* 3.0 45.1 + - + +
126B VAL* 1.3 74.7 - - - +
128B ASN* 1.3 62.8 + - - +
130B LEU* 3.1 19.4 + - + +
131B PHE* 3.3 31.0 - - + -
143B PHE* 3.6 13.0 - - + -
146B PHE* 4.0 18.4 - - + -
173B TYR* 3.3 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU* 2.7 51.9 + - - +
125B GLN* 3.8 13.5 - - - +
126B VAL 3.0 0.4 - - - -
127B VAL* 1.3 73.7 - - - +
129B GLU* 1.3 62.6 + - - +
131B PHE 3.5 1.0 + - - -
132B ARG* 3.1 27.9 + - - +
173B TYR* 2.8 31.4 + - - -
177B HIS* 3.9 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLN 4.2 12.5 - - - +
126B VAL* 2.8 13.0 + - - +
128B ASN* 1.3 80.6 - - - +
130B LEU* 1.3 66.5 + - - +
131B PHE 3.4 0.3 + - - -
132B ARG* 3.6 35.2 + - - +
133B ASP 5.2 0.2 + - - -
75C GLU* 4.0 15.1 - - - +
78C ARG* 3.4 31.7 + - - +
79C MET* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL 3.7 0.6 + - - -
127B VAL* 3.1 18.3 + - + +
129B GLU* 1.3 80.4 - - - +
131B PHE* 1.3 77.2 + - + +
132B ARG 3.8 0.2 + - - -
133B ASP 5.1 0.7 + - - -
134B GLY 4.4 0.2 - - - +
139B ARG* 3.7 50.4 + - + +
142B ALA* 4.1 12.3 - - + +
143B PHE* 4.0 17.5 - - + +
146B PHE* 5.7 3.1 - - + -
72C SER* 4.3 12.8 - - - +
75C GLU* 4.0 21.9 - - + +
76C LEU* 4.5 12.1 - - + -
79C MET* 3.6 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 3.3 40.3 + - + -
128B ASN 3.5 2.0 + - - +
129B GLU 3.2 0.2 - - - -
130B LEU* 1.3 84.0 - - + +
132B ARG* 1.3 57.5 + - - +
133B ASP 3.2 2.7 - - - -
134B GLY* 2.7 35.2 + - - +
135B VAL* 3.9 19.3 - - + +
139B ARG* 3.6 44.6 - - + -
140B ILE* 4.0 8.7 - - + -
143B PHE* 3.6 14.8 - - + -
173B TYR* 3.4 28.5 - + - +
177B HIS* 6.3 0.2 - - + -
178B LEU* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASN 3.1 13.2 + - - +
129B GLU* 3.6 36.8 + - - +
130B LEU 3.5 1.0 - - - -
131B PHE* 1.3 78.0 - - - +
133B ASP* 1.3 73.3 + - - +
134B GLY 3.3 2.3 + - - -
75C GLU* 6.3 0.2 - - - -
78C ARG* 5.6 5.1 - - - +
----------------------------------------------------------
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