Contacts of the helix formed by residues 93 - 102 (chain B) in PDB entry 2P1Q
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 93 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.1 2.7 - - + -
91B GLY 3.4 1.0 + - - -
92B TYR* 1.3 70.4 - - - +
94B TYR* 1.3 69.6 + - - +
95B PRO* 3.3 3.1 - - - -
96B TRP* 2.9 25.2 + - + -
97B ILE* 3.1 25.1 + - + -
112B LEU* 3.8 39.7 - - + -
115B MET* 3.6 22.0 - - + -
116B VAL 3.1 18.2 + - - +
117B VAL* 4.0 5.4 - - + -
121B CYS* 3.6 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 3.4 4.6 - - + +
93B VAL* 1.3 79.6 - - - +
95B PRO* 1.4 67.6 - - + +
97B ILE* 3.1 3.4 + - + -
98B GLU* 2.8 63.4 + - + +
116B VAL 4.7 0.2 + - - -
118B THR* 4.8 3.4 - - + +
120B ASP* 4.2 25.4 - - + -
121B CYS* 3.7 34.0 - - - -
124B LEU* 4.1 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PRO* 4.2 13.2 - - + +
92B TYR* 3.5 22.2 - - + +
93B VAL 3.4 4.3 - - - -
94B TYR* 1.4 96.5 - - + +
96B TRP* 1.3 57.4 + - + +
98B GLU* 3.6 9.6 + - + +
99B ALA* 3.0 30.3 + - - +
568B ASP* 6.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 4.4 4.9 - - + -
53B CYS* 3.3 36.2 + - - +
54B TYR* 6.2 1.2 - - - -
56B VAL* 3.6 18.6 - - + -
58B PRO* 3.5 46.0 - - + +
61B VAL* 3.8 29.6 - - + -
62B ILE* 6.2 1.3 - - + -
71B VAL* 5.3 5.6 - - + -
73B LEU* 3.7 45.8 - - + -
92B TYR 4.1 14.9 + - - -
93B VAL* 2.9 19.2 + - + +
95B PRO* 1.3 77.7 - - + +
97B ILE* 1.3 59.9 + - - +
99B ALA* 3.3 1.2 + - - +
100B MET* 2.9 47.8 + - + +
115B MET* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 3.1 39.3 + - + +
94B TYR* 3.7 5.8 - - + +
96B TRP* 1.3 74.0 - - - +
98B GLU* 1.3 54.9 + - - +
100B MET* 3.3 21.5 + - + +
101B SER* 2.7 37.8 + - - -
110B ILE* 4.1 12.3 - - + -
112B LEU* 5.4 1.1 - - + -
121B CYS* 3.9 15.0 - - + +
124B LEU* 3.7 30.7 - - + -
125B ILE* 3.9 33.7 - - + +
129B PHE* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 2.8 48.1 + - + +
95B PRO* 3.8 7.7 - - + +
97B ILE* 1.3 79.4 - - - +
99B ALA* 1.3 62.9 + - - +
101B SER* 2.6 22.3 + - - +
102B SER* 4.0 4.3 + - - -
124B LEU* 3.7 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PRO* 3.7 19.5 - - + -
59B ALA* 5.0 2.0 - - + +
62B ILE* 3.3 25.1 - - + +
95B PRO 3.0 17.4 + - - +
96B TRP 3.9 1.3 - - - +
98B GLU* 1.3 82.5 + - - +
100B MET* 1.3 60.9 + - - +
101B SER 3.5 0.2 + - - -
102B SER* 3.7 14.0 + - - -
103B SER* 3.8 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 3.8 12.1 - - + -
71B VAL* 3.7 31.6 - - + -
73B LEU* 5.2 2.0 - - + -
96B TRP* 2.9 41.7 + - + +
97B ILE* 3.9 22.4 - - + +
99B ALA* 1.3 74.1 - - - +
101B SER* 1.3 63.8 + - - +
103B SER 2.9 0.5 + - - -
104B TYR* 2.7 66.4 + - + +
107B LEU* 4.1 14.6 - - + -
110B ILE* 4.5 7.0 - - + -
129B PHE* 3.6 14.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 2.7 20.4 + - - -
98B GLU* 2.6 22.0 + - - +
99B ALA 3.3 0.2 - - - -
100B MET* 1.3 74.3 - - - +
102B SER* 1.3 60.5 + - - +
105B THR* 4.6 9.2 - - - +
124B LEU* 3.9 17.4 - - - +
128B SER* 3.4 32.5 - - - +
129B PHE* 3.7 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU 4.3 4.0 + - - -
99B ALA* 3.7 9.7 + - - -
100B MET 3.2 0.4 - - - -
101B SER* 1.3 82.3 + - - +
103B SER* 1.3 65.2 + - - +
105B THR* 4.3 10.6 - - - +
----------------------------------------------------------
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