Contacts of the helix formed by residues 75 - 84 (chain B) in PDB entry 6X34
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 75 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER* 1.3 76.5 - - - +
76B ARG* 1.3 63.3 + - + +
78B LEU* 3.7 6.6 - - - +
79B GLN* 2.9 29.6 + - - +
104B GLY 3.4 22.1 + - - +
106B ALA* 4.8 7.4 - - + +
149B THR* 4.3 19.7 - - + +
151B HIS* 5.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER* 3.3 5.2 - - - -
75B VAL* 1.3 83.5 - - + +
77B ALA* 1.3 59.8 + - - +
79B GLN* 3.3 5.8 + - - +
80B GLU* 2.9 29.6 + - - +
3927D ASP* 5.3 11.9 - - + +
3930D TRP* 4.0 28.4 - - + +
3931D TYR* 5.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.0 21.8 - - + -
74B SER* 3.4 13.4 + - - +
75B VAL 3.4 0.2 - - - -
76B ARG* 1.3 77.4 - - - +
78B LEU* 1.3 57.7 + - - +
80B GLU* 3.3 5.3 + - - +
81B MET* 2.9 31.1 + - - +
3930D TRP* 3.5 39.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.5 11.4 - - + +
74B SER 2.8 18.7 + - - +
75B VAL* 3.7 8.1 - - - +
76B ARG 3.3 0.2 - - - -
77B ALA* 1.3 77.0 - - - +
79B GLN* 1.3 56.8 + - - +
81B MET* 3.3 5.5 + - - +
82B LEU* 2.9 30.8 + - - +
106B ALA* 5.3 7.0 - - + -
147B TRP* 3.8 32.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL 2.9 18.6 + - - +
76B ARG* 3.3 6.3 + - - +
78B LEU* 1.3 75.1 - - - +
80B GLU* 1.3 58.0 + - - +
82B LEU* 3.4 5.3 + - - +
83B ALA* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG 2.9 17.0 + - - +
77B ALA* 3.8 7.2 - - - +
78B LEU 3.3 0.2 - - - -
79B GLN* 1.3 76.3 - - - +
81B MET* 1.3 61.9 - - - +
83B ALA* 3.5 6.3 + - - +
84B ASN* 3.3 23.4 + - - +
3930D TRP* 4.9 13.9 - - + +
3933D SER* 6.3 1.8 - - - -
3934D GLY* 5.7 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 6.3 3.1 - - + -
77B ALA 2.9 17.9 + - - +
78B LEU* 3.8 6.1 - - - +
79B GLN 3.3 0.2 - - - -
80B GLU* 1.3 77.9 - - - +
82B LEU* 1.3 57.4 + - - +
84B ASN* 3.0 26.0 + - - +
147B TRP* 5.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU 2.9 18.2 + - - +
79B GLN* 3.9 5.6 - - - +
81B MET* 1.3 73.9 - - - +
83B ALA* 1.3 65.1 + - - +
84B ASN 3.4 5.0 + - - +
143B GLY* 4.5 26.3 - - - +
147B TRP* 5.0 10.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLN 2.9 17.9 + - - +
80B GLU* 4.0 6.7 - - - +
81B MET 3.3 0.2 - - - -
82B LEU* 1.3 78.0 - - - +
84B ASN* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU 3.3 17.1 + - - +
81B MET* 3.0 19.0 + - - +
82B LEU 3.2 5.3 - - - +
83B ALA* 1.3 79.8 - - - +
----------------------------------------------------------
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