Contacts of the helix formed by residues 145 - 156 (chain C) in PDB entry 6B3I
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 SER 145 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 4.4 18.3 - - - +
144C THR* 1.3 79.5 + - - +
146C GLY* 1.3 70.2 + - - +
148C LEU* 3.7 11.3 + - - +
149C LYS* 3.3 20.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C SER* 1.3 82.7 + - - +
147C ASN* 1.3 64.5 + - - -
149C LYS* 3.2 14.8 + - - +
150C LYS* 3.4 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C GLY* 1.3 71.6 - - - -
148C LEU* 1.3 65.8 + - - +
150C LYS* 3.0 26.6 + - - +
151C ILE* 3.0 24.8 + - - +
188C THR* 4.5 6.3 - - - +
190C GLU* 2.9 38.9 + - + +
191C LEU* 4.3 10.7 - - - +
194C ASN* 4.0 6.0 + - - +
232C LEU* 3.8 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLU* 4.3 11.2 - - + -
110C ILE* 4.3 6.3 - - + -
144C THR* 4.2 20.2 - - + -
145C SER 3.7 8.0 + - - +
146C GLY 3.3 0.4 - - - -
147C ASN* 1.3 78.8 - - - +
149C LYS* 1.3 61.0 + - - +
151C ILE* 3.3 6.1 - - + +
152C LEU* 3.1 47.7 + - + +
231C ASP* 3.6 44.0 - - + +
232C LEU* 4.1 16.1 - - + +
235C ALA* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LYS* 3.5 43.2 + - - +
144C THR* 3.4 34.5 + - - +
145C SER* 3.3 15.8 + - - -
146C GLY 3.2 13.6 + - - +
147C ASN 3.2 0.2 - - - -
148C LEU* 1.3 80.0 - - - +
150C LYS* 1.3 62.3 + - + +
152C LEU* 4.9 0.9 - - - -
153C VAL* 3.1 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C GLY 3.4 5.9 + - - +
147C ASN* 3.0 32.8 + - - +
149C LYS* 1.3 81.6 - - + +
151C ILE* 1.3 57.3 + - - +
153C VAL* 3.9 2.8 - - - +
154C SER* 2.9 29.9 + - - -
191C LEU* 4.2 24.9 - - + +
194C ASN* 3.7 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ASN 3.0 12.1 + - - +
148C LEU* 3.3 27.8 - - + +
150C LYS* 1.3 76.5 - - - +
152C LEU* 1.3 63.2 + - + +
154C SER* 3.2 5.7 + - - -
155C LEU* 2.8 34.5 + - + +
193C PHE 5.1 0.4 - - - +
194C ASN* 3.7 36.6 - - + +
198C ALA* 3.7 29.4 - - + +
232C LEU* 4.3 10.1 - - + -
235C ALA* 4.6 7.4 - - + -
236C TYR* 4.5 4.7 - - + -
239C LEU* 4.1 25.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
106C GLU* 5.3 0.4 - - + +
109C LEU* 3.7 35.4 - - + +
110C ILE* 4.7 7.4 - - + -
113C LEU* 4.0 27.5 - - + +
114C CYS* 4.6 9.4 - - - -
140C VAL* 4.1 12.6 - - + -
144C THR* 4.1 8.3 - - + -
148C LEU* 3.1 45.9 + - + +
149C LYS* 4.3 0.9 - - - +
151C ILE* 1.3 76.6 - - + +
153C VAL* 1.3 65.8 + - - +
155C LEU* 3.2 15.5 + - + +
156C LEU* 3.0 28.1 + - - +
235C ALA* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLU* 3.6 26.0 - - + +
140C VAL* 4.3 13.7 - - + -
141C LYS* 3.7 35.4 - - + -
149C LYS* 3.1 25.6 + - + +
150C LYS* 4.0 3.4 - - - +
152C LEU* 1.3 74.3 - - - +
154C SER* 1.3 63.1 + - - +
156C LEU* 3.2 14.4 + - - +
157C GLN* 2.8 29.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
150C LYS 2.9 19.0 + - - -
151C ILE* 3.4 13.2 - - - -
153C VAL* 1.3 78.4 - - - +
155C LEU* 1.3 62.3 + - - +
157C GLN* 3.2 18.4 + - - +
159C ASN* 4.2 0.3 - - - +
194C ASN* 4.9 4.9 + - - -
198C ALA* 4.2 5.0 - - - +
199C LYS* 3.0 46.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 3.5 31.6 - - + +
114C CYS* 3.7 24.7 - - - -
121C ILE* 3.3 19.7 - - + +
151C ILE* 2.8 31.9 + - + +
152C LEU* 3.2 13.9 + - + +
154C SER* 1.3 75.7 - - - +
156C LEU* 1.3 60.8 + - - +
157C GLN 3.2 1.0 + - - -
158C ALA* 3.2 10.7 + - - -
160C ARG* 3.7 21.5 - - - +
198C ALA* 3.7 26.0 - - + +
199C LYS* 5.1 0.7 - - - +
239C LEU* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 3.7 28.5 - - + -
121C ILE* 4.0 6.6 - - + +
125C LYS* 2.8 49.0 + - + +
136C LEU* 3.8 19.7 - - + -
137C GLU* 3.7 37.0 - - + +
140C VAL* 4.1 22.2 - - + -
152C LEU 3.0 18.2 + - - +
153C VAL* 3.5 16.6 - - - +
154C SER 3.2 0.6 - - - -
155C LEU* 1.3 74.2 - - - +
157C GLN* 1.3 63.4 + - - +
158C ALA 3.1 1.1 + - - -
----------------------------------------------------------
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