Contacts of the helix formed by residues 143 - 154 (chain C) in PDB entry 3P3W
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 PHE 143 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN* 4.5 12.1 - - - -
139A THR* 5.1 8.7 - - + -
143A PHE* 4.1 30.7 - + - -
167A ASN* 5.9 1.1 - - - +
79C GLN* 4.6 17.9 - - - -
104C ASP* 2.9 11.0 + - - +
137C TYR* 6.2 4.3 - + - -
138C ASP 6.1 1.6 - - - -
139C THR* 5.6 12.3 - - + -
142C GLY* 1.3 73.8 - - - -
144C SER* 1.3 54.4 + - - +
145C VAL 3.3 2.9 - - - -
146C LEU* 3.3 25.5 + - + +
147C GLN* 2.8 56.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PRO 5.7 2.0 - - - -
103C THR 5.3 1.4 + - - -
104C ASP* 2.8 32.5 + - - -
118C LYS* 3.9 20.8 - - - +
141C ARG 5.4 2.5 - - - -
142C GLY 3.3 1.9 - - - -
143C PHE* 1.3 77.2 - - - +
145C VAL* 1.3 61.1 + - - +
147C GLN* 3.9 7.4 - - - +
148C ALA* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 5.1 11.9 - - + -
118C LYS* 4.9 24.7 - - + +
121C ILE* 5.3 11.2 - - + -
135C TYR* 3.4 17.3 - - + +
141C ARG* 5.4 11.4 - - + +
142C GLY 4.4 6.2 + - - +
143C PHE 3.3 0.2 - - - -
144C SER* 1.3 77.7 - - - +
146C LEU* 1.3 66.2 + - - +
148C ALA* 3.2 8.4 + - + +
149C ILE* 3.1 25.9 + - + +
192C ASP* 3.4 28.9 - - - +
220C ALA* 5.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C TYR* 3.5 38.9 + - + +
137C TYR* 4.0 29.2 - - + +
142C GLY 4.9 2.6 + - - +
143C PHE* 3.3 30.8 + - + +
145C VAL* 1.3 78.6 - - - +
147C GLN* 1.3 60.9 + - + +
149C ILE* 3.3 6.9 + - + +
150C MET* 2.9 53.6 + - + +
162C ALA* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASN* 3.9 39.7 + - - +
104C ASP* 5.0 2.4 - - - +
143C PHE* 2.8 43.7 + - + +
144C SER* 3.9 6.8 + - - +
146C LEU* 1.3 72.5 - - + +
148C ALA* 1.3 59.6 + - - +
149C ILE 3.2 0.4 - - - -
150C MET* 4.3 10.1 - - + -
151C GLU* 2.8 50.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LYS* 3.7 36.3 - - + +
122C LEU* 3.5 18.6 - - + +
144C SER 3.0 18.6 + - - +
145C VAL* 3.2 8.7 + - + +
147C GLN* 1.3 75.6 - - - +
149C ILE* 1.3 61.8 + - + +
151C GLU* 4.9 2.8 - - - +
152C ALA* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 4.6 9.2 - - + -
122C LEU* 5.8 4.3 - - + -
125C LEU* 4.3 17.7 - - + -
133C PHE* 4.7 12.3 - - + -
135C TYR* 4.2 27.1 - - + -
145C VAL* 3.1 17.3 + - + +
146C LEU* 3.4 9.9 - - + +
147C GLN 3.2 0.2 - - - -
148C ALA* 1.3 77.7 - - + +
150C MET* 1.3 58.6 + - + +
152C ALA* 3.2 3.7 + - - +
153C ALA* 2.8 38.2 + - + +
160C VAL* 4.5 22.0 - - + -
162C ALA* 6.3 1.3 - - + -
190C LEU* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 5.8 2.0 - - - +
164A SER* 5.1 22.4 - - - +
167A ASN* 5.6 5.8 - - - -
146C LEU* 2.9 48.2 + - + +
147C GLN* 3.3 9.4 + - + +
149C ILE* 1.3 79.7 - - + +
151C GLU* 1.3 61.9 + - + +
152C ALA 3.5 0.3 + - - -
153C ALA* 3.5 15.8 + - - +
154C VAL* 3.9 14.7 + - - +
162C ALA* 5.2 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASN* 5.7 3.5 - - - +
168A ILE* 5.4 8.0 - - - +
173A GLU* 4.8 13.6 - - - +
147C GLN* 2.8 38.9 + - + +
148C ALA* 4.9 3.4 - - - +
150C MET* 1.3 74.9 - - + +
152C ALA* 1.3 57.3 + - + +
153C ALA 3.5 0.2 - - - -
154C VAL* 3.4 14.4 - - - +
155C GLN* 3.4 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 3.8 19.5 - - + -
148C ALA 3.3 20.3 + - - +
149C ILE* 3.2 4.3 + - - +
151C GLU* 1.3 76.0 - - - +
153C ALA* 1.3 64.2 + - - +
154C VAL 3.2 2.5 - - - -
155C GLN* 3.4 15.6 + - + +
156C ASN* 3.2 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ILE* 2.8 18.3 + - + +
150C MET* 3.8 10.3 - - - +
152C ALA* 1.3 78.8 - - - +
154C VAL* 1.3 59.0 + - + +
157C ASN* 3.1 8.5 + - - -
158C TRP* 3.0 53.0 + - + +
160C VAL* 4.8 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 6.0 3.4 - - + -
180A GLU* 4.9 13.0 - - - +
150C MET 3.9 12.1 - - - +
151C GLU* 3.4 24.9 - - - +
153C ALA* 1.3 77.8 - - + +
155C GLN* 1.3 66.8 + - + +
156C ASN 3.5 0.2 - - - -
157C ASN* 4.1 5.7 + - - +
----------------------------------------------------------
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