Contacts of the helix formed by residues 151 - 167 (chain C) in PDB entry 2W4V
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 HIS 151 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TYR* 4.3 2.7 - - - -
13C LEU* 3.7 13.0 - - + -
113C TYR* 2.7 19.5 - - + -
115C TYR* 2.7 18.8 + - - -
131C ILE* 2.9 44.2 + - + +
140C TYR* 6.0 2.0 - - + -
148C ILE* 6.0 0.7 - - + -
149C PRO 3.4 4.5 + - - +
150C PRO* 1.3 74.3 - - - +
152C LEU* 1.3 65.4 + - + +
153C PHE* 1.7 71.3 + + + +
154C SER* 3.2 19.1 + - - +
155C VAL 3.4 1.9 + - - -
188C LYS* 2.9 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C TYR* 3.9 13.4 - - + +
120C CYS* 3.7 29.4 - - - -
122C ALA* 5.1 7.6 - - + -
151C HIS* 1.3 80.0 + - + +
153C PHE* 1.3 66.4 + - - +
155C VAL* 3.1 9.0 + - + +
156C ALA* 3.0 21.0 + - - +
185C ASN* 3.0 51.6 - - + +
188C LYS* 4.9 15.5 - - + +
189C VAL* 4.9 12.8 - - + +
668C VAL* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ILE 3.6 9.4 - - - -
132C TYR* 3.8 17.5 - - - -
136C VAL* 4.6 6.3 - - + -
137C ILE* 4.3 20.6 - - + -
140C TYR* 2.3 52.3 - + + -
151C HIS* 1.7 61.4 + + + +
152C LEU* 1.3 71.8 - - - +
154C SER* 1.3 49.7 + - - +
156C ALA* 3.0 1.9 + - - +
157C ASP 2.5 34.5 + - - -
188C LYS* 2.6 35.0 - - + -
191C MET* 6.4 0.2 - - + -
192C TYR* 3.5 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C TYR* 3.1 22.9 + - - -
140C TYR* 3.5 5.2 - - - +
143C LYS 5.3 1.6 - - - -
145C LYS* 4.9 4.3 - - - -
148C ILE* 3.6 32.1 - - - +
149C PRO 3.8 7.2 + - - -
151C HIS* 3.2 8.4 + - - +
153C PHE* 1.3 79.0 - - - +
155C VAL* 1.3 54.8 + - - +
157C ASP* 3.8 6.2 - - - +
158C ASN* 2.6 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C TYR* 2.9 30.5 - - + +
115C TYR* 3.9 5.4 - - + +
120C CYS* 3.7 17.0 - - + +
145C LYS* 5.0 8.9 - - - +
151C HIS 3.4 6.0 + - - +
152C LEU* 3.1 11.6 + - + +
154C SER* 1.3 76.5 - - - +
156C ALA* 1.3 57.8 + - - +
158C ASN* 3.7 6.0 - - - +
159C ALA* 3.1 26.5 + - - +
172C CYS* 5.6 2.0 - - + -
666C HIS* 4.0 29.6 + - + +
667C PHE 5.3 0.7 - - - +
668C VAL* 4.5 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU 3.0 10.0 + - - +
153C PHE 3.0 2.8 + - - +
155C VAL* 1.3 74.9 - - - +
157C ASP* 1.3 63.8 + - - +
159C ALA* 3.1 8.4 + - - +
160C TYR 3.0 14.2 + - - -
189C VAL* 4.0 20.9 - - + -
192C TYR* 2.1 65.9 + - + -
666C HIS* 5.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C TYR* 2.8 43.1 + - + +
141C ARG* 3.3 2.3 - - - +
142C GLY* 2.7 41.2 + - - -
143C LYS 3.7 9.8 + - - +
153C PHE 2.5 20.5 + - - +
154C SER* 3.8 5.6 - - - +
156C ALA* 1.3 70.7 - - - +
158C ASN* 1.3 64.0 + - - +
160C TYR* 3.2 9.5 + - - +
161C GLN* 3.2 21.5 + - - +
192C TYR* 3.0 4.4 - - - -
196C VAL* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LYS 3.9 13.7 + - - +
144C ARG* 4.3 3.6 - - - -
145C LYS* 2.6 60.0 + - - +
154C SER* 2.6 33.8 + - - +
155C VAL 3.7 3.6 - - - +
156C ALA 3.1 0.2 - - - -
157C ASP* 1.3 72.2 - - - +
159C ALA* 1.3 62.0 + - - +
160C TYR 3.1 0.3 + - - -
161C GLN* 3.1 8.9 + - - +
162C ASN* 2.7 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL 3.1 8.8 + - - +
156C ALA* 3.6 8.5 - - - +
158C ASN* 1.3 75.3 - - - +
160C TYR* 1.3 62.3 + - - +
162C ASN* 3.4 9.5 + - - +
163C MET* 2.9 29.1 + - - +
170C GLN* 3.0 11.6 - - + +
192C TYR* 5.4 0.2 - - - +
456C ILE* 4.6 6.1 - - + -
666C HIS* 2.7 46.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ALA 3.0 11.5 + - - +
157C ASP* 3.3 14.8 - - - +
158C ASN 3.0 0.6 - - - -
159C ALA* 1.3 77.4 - - - +
161C GLN* 1.3 68.7 + - + +
163C MET* 3.1 11.0 + - + +
164C VAL* 3.0 44.0 + - + +
192C TYR* 3.9 11.4 + - + +
193C LEU* 5.5 1.1 - - + -
196C VAL* 5.9 12.3 - - + -
251C PHE* 3.9 28.5 - + - -
254C THR 4.5 0.7 + - - -
255C GLY* 2.2 44.0 + - - -
454C TYR* 3.2 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C GLY* 6.4 2.2 - - - -
157C ASP* 3.2 11.5 + - - +
158C ASN* 3.1 14.0 + - - +
160C TYR* 1.3 85.3 - - + +
162C ASN* 1.3 62.6 + - - +
164C VAL* 3.3 4.0 + - + +
165C THR* 2.7 63.7 + - + +
166C ASP* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C LYS* 6.1 0.4 - - - +
158C ASN* 2.7 32.7 + - - +
159C ALA* 3.6 5.6 - - - +
161C GLN* 1.3 80.5 + - - +
163C MET* 1.3 57.7 + - - +
166C ASP* 2.6 55.3 + - - +
168C GLU* 4.5 0.2 - - - +
170C GLN* 2.5 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ALA 2.9 7.1 + - - +
160C TYR* 3.5 11.2 - - + +
162C ASN* 1.3 75.1 - - - +
164C VAL* 1.3 54.1 + - - +
167C ARG* 2.8 31.5 + - - -
168C GLU* 3.2 15.1 + - - +
170C GLN* 2.1 50.9 - - + +
251C PHE* 3.8 9.9 - - + -
454C TYR* 2.6 64.5 - - + +
455C TYR 2.6 28.5 - - - +
456C ILE* 3.3 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C TYR* 3.0 40.4 + - + +
161C GLN* 3.4 8.3 - - - +
163C MET* 1.3 78.0 - - - +
165C THR* 1.3 74.3 + - + +
167C ARG* 3.3 19.1 + - - +
255C GLY* 5.4 3.4 - - - -
454C TYR* 3.1 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C GLN* 2.7 60.1 + - + +
164C VAL* 1.3 78.1 - - + +
166C ASP* 1.3 75.1 + - - -
167C ARG* 2.4 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C GLN* 4.7 0.2 - - - +
162C ASN* 2.6 51.7 + - - +
165C THR* 1.3 80.8 + - - +
167C ARG* 1.3 70.6 + - - +
168C GLU* 4.2 15.3 - - + +
664C HIS* 5.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C MET 2.8 16.3 + - - -
164C VAL 3.3 11.8 + - - +
165C THR* 2.4 35.5 + - - +
166C ASP* 1.3 80.6 - - - +
168C GLU* 1.3 59.0 + - - +
454C TYR* 5.6 3.1 - - - -
----------------------------------------------------------
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