Contacts of the strand formed by residues 75 - 79 (chain C) in PDB entry 2IHU
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 GLN 75 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLY 5.3 2.6 - - - +
27C VAL* 4.4 20.2 - - - +
28C GLY 4.8 3.0 - - - +
29C LYS* 4.5 6.5 + - - +
31C PHE* 5.3 1.3 - - + -
64C ALA* 3.5 24.2 - - + +
67C LEU* 3.6 28.7 - - + +
68C ALA* 3.4 26.5 - - + +
71C THR* 3.4 18.9 + - - +
73C ARG* 3.5 14.2 + - - +
74C PRO* 1.3 84.6 + - - +
76C ALA* 1.3 58.9 + - - +
101C PRO 3.2 6.6 + - - +
102C VAL* 3.5 3.4 - - + -
103C ILE* 2.7 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 4.5 14.1 - - + -
27C VAL* 4.1 19.7 - - + -
29C LYS 3.9 7.4 + - - +
30C VAL* 3.6 14.9 - - + -
31C PHE* 3.1 30.6 + - - -
64C ALA* 4.0 3.8 - - - +
75C GLN* 1.3 79.8 - - - +
77C CYS* 1.3 62.1 + - - +
102C VAL* 5.0 0.2 - - - -
103C ILE* 3.2 15.9 - - + +
105C LEU* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 4.2 2.7 - - - -
31C PHE 3.0 13.5 - - - +
60C ALA 3.8 17.5 - - - +
61C GLY* 3.9 9.4 - - - -
64C ALA* 4.1 1.6 - - + -
76C ALA* 1.3 75.8 - - - +
78C TRP* 1.3 61.6 + - - +
88C LEU* 3.7 25.8 - - + -
92C ILE* 5.4 2.2 - - - -
102C VAL* 3.9 24.2 - - - -
103C ILE 3.0 7.6 + - - +
104C ALA* 3.9 15.0 - - - -
105C LEU* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 3.7 23.6 - - + -
19C LEU* 6.0 0.9 - - + -
30C VAL* 3.8 15.7 - - + -
31C PHE 2.7 9.2 + - - +
32C GLY* 3.1 19.8 - - - -
33C VAL 3.3 22.1 + - - -
34C VAL* 4.4 4.0 - - + +
37C GLU* 2.9 31.4 + - + +
41C ILE* 3.8 32.5 - - + -
43C PHE* 3.5 29.7 - + - -
51C PHE* 4.0 6.7 - - + -
57C GLU* 4.5 1.6 - - - +
77C CYS* 1.3 76.6 - - - +
79C ALA* 1.3 83.1 + - - +
88C LEU* 4.3 6.7 - - - +
105C LEU* 3.3 28.7 - - + -
107C ALA* 4.9 4.5 - - + -
168C LEU* 3.5 26.2 - - + -
173C LEU* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL 3.6 7.4 - - - -
57C GLU* 3.8 11.4 - - + -
78C TRP* 1.3 88.3 + - - +
80C THR* 1.3 60.7 + - - +
84C GLY 3.2 31.0 - - - +
85C MET* 3.9 2.9 - - - +
88C LEU* 3.9 16.6 - - + -
105C LEU 3.0 7.0 + - - +
106C ALA* 3.0 5.7 - - + -
107C ALA 3.0 21.3 + - - -
----------------------------------------------------------
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