Contacts of the helix formed by residues 65 - 70 (chain B) in PDB entry 2A1H
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 65 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.4 9.4 - - - +
62B HIS* 2.9 21.6 + - - -
63B PRO 3.3 1.0 - - - -
64B ALA* 1.3 73.3 - - - +
66B SER* 1.3 58.6 + - - +
67B SER* 2.8 30.1 + - - -
68B LEU* 3.0 19.6 + - - +
69B HIS* 3.3 12.6 - - - -
148B GLY 3.5 4.7 + - - -
149B ASN* 2.8 27.3 + - - -
150B GLU 3.4 10.5 - - - -
151B PRO* 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA 3.1 6.2 + - - -
65B SER* 1.3 70.6 + - - +
67B SER* 1.3 57.8 + - - +
68B LEU 3.2 0.4 - - - -
69B HIS* 4.0 3.6 - - - +
70B TYR* 3.1 38.8 + - - +
72B LEU* 3.5 34.7 + - - +
148B GLY* 3.6 9.9 - - - -
150B GLU* 3.1 35.1 + - - +
152B SER 4.6 5.2 - - - -
154B GLY 5.5 2.7 - - - -
156B SER 5.6 1.1 - - - -
158B PRO* 3.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER 4.2 0.9 - - - +
68A LEU* 3.7 19.0 - - - +
73A GLN* 2.9 19.1 + - - +
61B LEU* 4.2 1.4 - - - +
65B SER* 2.8 21.7 + - - -
66B SER* 1.3 76.8 - - - +
68B LEU* 1.3 62.7 + - - +
71B SER* 3.8 2.8 - - - -
72B LEU 3.7 12.3 - - - +
73B GLN* 3.0 14.2 - - - +
147B ILE* 3.8 24.1 - - - +
148B GLY 3.1 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.6 32.1 - - + -
61A LEU* 4.0 14.4 - - + -
67A SER* 3.5 34.1 - - - +
68A LEU* 3.9 16.6 - - + -
73A GLN* 3.1 30.9 + - - +
74A LEU 5.1 1.0 + - - +
145A VAL* 4.2 10.4 - - - +
147A ILE* 4.2 11.6 - - + +
164A PHE* 4.6 7.4 - - + -
61B LEU* 4.3 8.7 - - + -
62B HIS 4.8 2.0 - - - +
63B PRO 5.1 1.1 - - - +
65B SER* 3.0 15.7 + - - +
67B SER* 1.3 86.6 + - - +
69B HIS* 1.3 63.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 3.4 3.8 + - - -
74A LEU 5.8 0.2 - - - -
75A PHE* 3.4 17.0 - - + +
143A ARG* 3.0 38.3 + - + +
145A VAL* 3.5 27.5 - - + +
164A PHE* 4.3 1.6 - - - -
166A ILE* 4.2 4.3 - - + -
204A GLY* 3.2 17.8 - - - -
63B PRO 2.7 27.0 + - - -
64B ALA* 3.6 8.9 - - - +
65B SER 3.3 19.6 + - - +
66B SER* 4.7 1.6 - - - +
68B LEU* 1.3 85.7 - - + +
70B TYR* 1.3 79.8 + - + +
153B LEU* 3.6 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PHE* 3.8 14.1 - + - -
143A ARG* 2.9 33.4 + - - -
204A GLY 3.2 8.0 - - - +
207A TYR* 3.8 25.8 - + + -
208A GLY* 2.9 26.4 + - - +
502A GBN 3.4 18.5 - - + +
66B SER* 3.1 21.4 + - - +
69B HIS* 1.3 90.0 - - + +
71B SER* 1.3 67.7 + - - +
72B LEU* 3.3 13.5 + - + +
152B SER 4.5 2.7 - - - -
153B LEU* 2.5 37.2 + - - -
154B GLY 3.6 18.6 - - - -
155B VAL* 3.8 17.0 - - + -
156B SER 5.4 0.2 - - - -
----------------------------------------------------------
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