Contacts of the strand formed by residues 92 - 98 (chain B) in PDB entry 1H4R
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 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 3.8 34.1 - - + -
23B THR 3.0 6.4 + - - +
24B VAL* 3.1 11.5 - - + +
25B ARG 2.8 19.9 + - - -
81B VAL* 5.0 2.0 - - + -
82B LEU* 4.3 7.2 - - + -
86B VAL* 4.1 13.7 - - + -
87B SER* 3.7 24.9 - - - +
88B LYS 4.0 10.5 - - - +
89B GLU 3.7 10.8 - - - +
90B GLU* 3.8 1.5 - - + +
91B PRO* 1.3 69.4 - - - +
93B THR* 1.3 60.7 + - - +
94B PHE* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.3 25.0 - - + +
27B VAL* 4.0 22.4 - - + -
65B GLN 4.4 1.6 - - - +
66B TYR* 4.6 6.2 - - - +
86B VAL* 4.6 6.4 - - - +
91B PRO* 3.2 16.1 + - - +
92B VAL* 1.3 74.8 - - - +
94B PHE* 1.3 78.1 + - - +
95B HIS* 4.4 10.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.8 19.1 - - + -
25B ARG 2.9 6.5 + - - +
26B ILE* 3.4 8.4 - - + -
27B VAL* 2.9 26.2 + - - +
46B LEU* 4.0 12.3 - - + -
64B LEU* 3.9 24.7 - - + -
65B GLN 3.3 14.8 - - - +
66B TYR* 4.0 19.7 - + + -
75B LEU* 3.6 43.5 - - + -
81B VAL* 4.0 16.4 - - + -
86B VAL* 4.4 10.5 - - + -
92B VAL* 3.7 28.5 - - + -
93B THR* 1.3 80.2 - - - +
95B HIS* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 3.4 41.0 - - + +
64B LEU* 3.5 1.5 - - - -
65B GLN* 2.7 51.7 + - + +
93B THR* 4.4 11.1 + - + +
94B PHE* 1.3 76.5 - - - +
96B PHE* 1.3 60.7 + - - +
97B LEU* 3.4 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 3.9 18.8 - - + -
27B VAL 2.8 16.6 + - - +
28B THR* 3.9 15.7 - - + -
29B MET* 4.5 2.8 + - - +
47B PHE* 3.8 23.8 - + - -
50B VAL* 3.7 21.8 - - + -
51B CYS* 3.9 16.8 - - - -
54B LEU* 3.6 25.8 - - + -
56B LEU* 4.2 6.5 - - + -
62B PHE* 3.6 35.7 - + + -
63B GLY 3.5 6.7 - - - -
64B LEU* 3.9 14.8 - - + +
94B PHE 3.9 2.0 + - - -
95B HIS* 1.3 69.2 - - - +
97B LEU* 1.3 68.7 + - - +
117B LEU* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL 5.7 0.4 - - - +
28B THR 6.0 0.4 - - - -
29B MET* 3.9 24.9 - - + +
62B PHE* 3.4 9.4 - - - -
63B GLY 3.0 31.1 + - - +
65B GLN* 3.7 34.5 - - + +
74B TRP* 3.8 13.1 - - + -
95B HIS* 3.4 23.3 + - + +
96B PHE* 1.3 83.3 - - - +
98B ALA* 1.3 63.9 + - - +
99B LYS 3.4 0.5 + - - -
121B GLN* 3.5 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE 3.4 6.1 - - - +
62B PHE* 3.6 15.0 - - + -
74B TRP* 3.8 7.0 - - - -
97B LEU* 1.3 71.2 - - - +
99B LYS* 1.3 59.8 + - - +
100B PHE 3.8 3.8 - - - +
101B TYR* 4.2 7.0 + - + -
118B PHE* 3.6 40.6 - - + -
121B GLN* 2.9 34.9 + - - +
----------------------------------------------------------
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