Contacts of the helix formed by residues 154 - 165 (chain A) in PDB entry 3CJR
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 VAL 154 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 3.8 24.0 - - + -
130A GLY* 3.5 27.6 - - - +
149A ASP* 3.6 25.8 - - + +
151A ASP* 3.3 35.2 - - + +
153A MET* 1.3 77.4 - - + +
155A LEU* 1.3 63.4 + - + +
156A PRO 3.5 0.2 - - - -
157A GLN* 3.1 14.2 + - - +
158A ALA* 2.9 26.7 + - - +
255A SFG 4.6 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A THR* 4.6 7.9 - - + -
149A ASP* 4.3 17.3 - - + +
151A ASP 4.2 2.7 - - - +
152A PRO* 3.5 24.7 - - + +
154A VAL* 1.3 76.4 - - + +
156A PRO* 1.4 68.4 - - + +
158A ALA* 3.2 5.1 + - - +
159A GLU* 3.0 31.0 + - + +
171A PHE* 4.3 13.0 - - + -
172A LEU* 3.8 27.4 - - - +
173A GLU* 3.6 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PRO 3.4 14.4 - - - +
153A MET* 3.4 15.9 - - + +
155A LEU* 1.4 90.5 - - + +
157A GLN* 1.3 57.3 + - + +
159A GLU* 3.5 7.9 + - + +
160A ALA* 3.1 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 5.3 5.3 + - - +
96A GLY* 4.5 13.5 - - - +
97A MET* 4.6 2.7 + - - +
98A ALA* 3.6 36.6 + - + +
131A SER* 4.2 4.3 - - - +
153A MET* 3.6 17.5 - - - +
154A VAL* 3.1 11.4 + - - +
156A PRO* 1.3 76.0 - - + +
158A ALA* 1.3 61.1 + - - +
160A ALA* 3.4 6.1 + - - +
161A ASN* 3.0 39.7 + - - +
164A ARG* 4.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A THR* 4.7 2.0 - - + -
130A GLY 3.7 13.7 - - - +
131A SER 3.3 15.8 + - - +
136A ILE* 4.2 0.7 - - - +
154A VAL 2.9 13.3 + - - +
155A LEU* 3.2 11.0 + - - +
157A GLN* 1.3 76.4 - - - +
159A GLU* 1.3 56.6 + - - +
161A ASN* 3.4 3.1 + - - +
162A ALA 3.0 23.2 + - - -
171A PHE* 3.4 41.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 3.0 22.6 + - + +
156A PRO* 3.8 7.4 - - + +
158A ALA* 1.3 72.5 - - - +
160A ALA* 1.3 64.7 + - - +
162A ALA* 3.3 6.8 + - - +
163A LYS* 3.2 43.9 + - - +
169A PRO 4.7 5.2 - - - +
171A PHE* 3.6 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PRO 3.1 19.0 + - - +
157A GLN* 3.7 7.4 - - - +
158A ALA 3.3 0.2 - - - -
159A GLU* 1.3 73.7 - - - +
161A ASN* 1.3 65.3 + - - +
163A LYS* 3.3 10.8 + - - +
164A ARG* 3.2 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL 3.9 1.3 - - - +
93A ILE* 3.6 18.3 - - + +
94A GLU* 2.9 32.0 + - - +
131A SER* 2.9 33.8 + - - +
136A ILE* 3.6 18.4 - - + -
157A GLN* 3.0 22.3 + - - +
158A ALA 3.6 2.2 - - - +
159A GLU 3.3 0.2 - - - -
160A ALA* 1.3 75.5 - - - +
162A ALA* 1.3 58.8 + - - +
164A ARG* 2.9 24.5 + - - +
165A ASN* 2.8 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 3.5 12.9 - - + +
158A ALA 3.0 15.1 + - - +
159A GLU* 3.5 13.7 - - - +
160A ALA 3.3 0.2 - - - -
161A ASN* 1.3 75.1 - - - +
163A LYS* 1.3 58.0 + - + +
165A ASN* 2.9 17.7 + - - +
166A GLY 3.1 9.4 + - - -
167A VAL* 3.3 27.4 + - - +
168A ARG* 5.0 0.9 - - + -
169A PRO* 3.9 18.6 - - + -
171A PHE* 4.0 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLU* 3.2 30.4 + - - +
160A ALA* 3.8 10.5 - - - +
161A ASN 3.3 0.2 - - - -
162A ALA* 1.3 79.3 - - + +
164A ARG* 1.3 62.0 + - - +
165A ASN 3.1 0.7 + - - -
166A GLY* 3.5 10.5 + - - +
167A VAL 4.8 1.6 - - - +
168A ARG* 6.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO* 4.0 16.2 - - - +
92A VAL* 3.9 39.1 - - + +
94A GLU* 3.4 28.1 + - - +
157A GLN 4.7 0.6 + - - -
160A ALA* 3.2 24.0 + - - +
161A ASN* 2.9 52.7 + - - +
163A LYS* 1.3 76.2 - - + +
165A ASN* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO 3.7 6.8 - - - +
91A LEU* 3.6 7.1 - - - -
92A VAL* 2.8 48.5 + - - +
93A ILE* 4.7 0.6 - - - +
136A ILE* 3.6 33.7 - - + +
140A LYS* 2.8 36.2 + - - +
161A ASN 2.8 23.2 + - - -
162A ALA 2.9 8.2 + - - +
164A ARG* 1.3 80.4 - - - +
166A GLY* 1.3 62.1 + - - +
167A VAL* 3.2 2.5 + - + +
----------------------------------------------------------
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