Contacts of the helix formed by residues 71 - 78 (chain D) in PDB entry 2V3W
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 71 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ASN* 3.7 6.5 - - - -
28D GLU* 3.7 0.2 + - - -
69D LEU 3.6 3.6 + - - -
70D HIS* 1.3 78.0 - - - +
72D ALA* 1.3 63.5 + - - +
73D ALA 4.6 0.4 - - - -
75D THR* 2.6 33.3 + - - -
96D ALA* 4.0 2.1 - - - +
97D GLY 3.1 28.1 + - - +
110D LEU* 2.9 45.2 + - - +
111D THR 3.9 1.0 - - - -
112D ASN* 3.6 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET 5.1 0.2 - - - +
80B GLY* 4.5 1.0 - - - -
83B SER* 4.5 17.5 - - - -
122B LEU* 5.1 6.5 - - + +
400B ALA* 6.5 0.2 - - + -
71D SER* 1.3 83.7 + - - +
73D ALA* 1.3 56.1 + - - +
76D GLY* 2.7 33.6 + - - -
111D THR 4.6 3.8 - - - +
112D ASN* 3.4 26.7 - - - +
113D VAL 5.2 0.4 - - - +
118D LEU* 3.7 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY* 3.5 8.3 - - - +
83B SER* 3.9 16.4 + - - +
400B ALA 4.8 4.7 - - - +
401B GLY 4.8 0.7 - - - -
402B GLY* 3.4 35.2 - - - +
1531B TPP 4.0 12.8 - - + +
70D HIS 3.9 2.4 + - - +
71D SER* 3.5 1.0 - - - -
72D ALA* 1.3 79.3 - - - +
74D GLY* 1.3 57.7 + - - +
76D GLY 3.4 0.2 + - - -
77D ASN* 3.0 33.8 + - - +
110D LEU* 5.1 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1531B TPP 4.0 1.0 - - - +
47D GLU* 3.2 52.8 - - - +
69D LEU* 3.8 6.7 - - - +
70D HIS 2.9 23.6 + - - -
73D ALA* 1.3 73.7 - - - +
75D THR* 1.3 66.8 + - - +
77D ASN 3.5 4.0 + - - -
78D ALA 3.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 4.1 13.6 - - + +
71D SER 2.6 24.4 + - - -
72D ALA 3.8 3.1 - - - -
74D GLY* 1.3 75.4 - - - +
76D GLY* 1.3 64.5 + - - +
78D ALA* 3.2 13.3 + - - +
79D MET* 3.2 17.1 + - + +
82D LEU* 5.1 5.7 - - + +
94D VAL* 5.7 0.4 - - + -
96D ALA* 3.4 10.4 - - - +
118D LEU* 3.8 19.7 - - + -
119D PRO* 4.7 7.4 - - + -
155D TYR* 2.9 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLY 2.9 25.1 - - - +
79B MET* 3.5 14.0 - - - +
80B GLY 3.3 19.1 - - - -
72D ALA 2.7 21.9 + - - -
75D THR* 1.3 74.1 - - - +
77D ASN* 1.3 59.3 + - - +
78D ALA 3.0 1.6 + - - -
79D MET* 3.2 10.6 + - - +
118D LEU* 4.3 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN* 5.2 0.5 + - - -
48B ALA* 4.7 5.7 - - - +
76B GLY 4.7 1.3 - - - -
77B ASN* 4.5 18.1 - - - +
80B GLY* 3.3 19.2 + - - +
81B ALA 4.0 2.1 + - - -
403B LEU 4.0 10.8 + - - +
433B TYR* 4.2 2.4 - - - +
1531B TPP 3.2 22.8 - - - +
46D GLN* 3.4 26.5 + - - +
47D GLU* 3.0 27.6 + - + +
48D ALA* 3.6 20.4 - - - +
73D ALA* 3.0 13.0 + - - +
74D GLY 3.8 3.8 - - - +
75D THR 3.4 0.4 - - - -
76D GLY* 1.3 74.0 - - - +
78D ALA* 1.3 56.8 + - - +
79D MET 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLU 3.4 13.0 - - - +
48D ALA* 4.2 3.4 - - - +
51D VAL* 3.3 28.7 - - + -
69D LEU* 3.8 15.3 - - + -
74D GLY 3.5 3.1 + - - +
75D THR 3.2 10.8 + - - +
76D GLY 3.0 1.4 + - - -
77D ASN* 1.3 76.6 - - - +
79D MET* 1.3 58.3 + - - +
80D GLY 3.4 2.9 - - - -
81D ALA* 3.2 7.7 + - - +
82D LEU* 3.0 30.8 + - + +
----------------------------------------------------------
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