Contacts of the strand formed by residues 94 - 100 (chain B) in PDB entry 3A7H
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 LYS 94 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 3.8 25.4 - - + -
55B ILE 3.3 4.9 - - - +
56B ASP* 3.5 29.0 + - + +
59B GLU* 5.6 0.2 - - - -
89B TYR 3.8 0.5 - - - +
90B LEU* 3.6 3.9 - - - -
91B LYS* 2.9 39.1 + - + +
92B ASP* 3.3 2.8 - - + +
93B THR* 1.3 90.9 + - - +
95B LEU* 1.3 61.3 + - - +
96B TRP* 3.9 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.1 15.5 - - + -
13B MET* 3.9 26.9 - - + -
53B LYS 3.4 2.1 - - - +
54B ILE* 3.2 4.7 - - - -
55B ILE* 2.8 46.1 + - + +
57B LEU* 4.1 27.1 - - + -
67B ILE* 4.5 12.3 - - + -
88B SER* 4.1 8.3 - - - -
89B TYR 3.3 17.3 - - - +
90B LEU* 4.0 8.5 - - + +
93B THR 4.0 0.8 + - - -
94B LYS* 1.3 72.6 - - - +
96B TRP* 1.4 58.2 + - - +
97B ILE* 4.0 28.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
20B PRO* 3.6 50.6 - - + +
21B GLU* 3.5 36.7 + - + +
24B PHE* 4.3 7.6 - + + -
26B LYS* 4.1 23.3 - - + -
52B ILE* 3.5 37.0 - - + -
53B LYS 3.5 4.5 - - - -
54B ILE* 3.4 35.1 - - + +
88B SER* 3.2 5.4 - - - -
89B TYR* 2.7 38.2 + - + +
91B LYS* 4.4 8.4 - - + +
94B LYS* 3.9 14.9 + - - +
95B LEU* 1.4 74.2 - - - +
97B ILE* 1.3 62.4 + - - +
98B ILE* 3.8 8.9 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
51B ALA 3.6 1.2 - - - +
52B ILE* 3.4 4.7 - - - -
53B LYS* 2.7 56.9 + - + +
55B ILE* 3.8 27.1 - - + -
67B ILE* 4.2 4.9 - - + -
71B ILE* 3.7 26.5 - - + -
85B TYR* 3.8 26.7 - - + -
87B GLY 4.0 2.0 - - - -
88B SER* 4.3 3.4 - - - +
95B LEU* 4.1 20.6 - - + +
96B TRP* 1.3 74.7 - - - +
98B ILE* 1.3 62.8 + - - +
99B MET* 3.9 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.8 34.5 - - + -
50B VAL* 3.9 25.8 - - + -
51B ALA 3.7 1.6 - - - -
52B ILE* 4.0 26.5 - - + -
85B TYR* 3.6 4.2 - - - -
86B TYR* 2.8 44.2 + - + +
87B GLY 2.9 17.3 + - - +
89B TYR* 3.6 25.4 - - + -
96B TRP* 4.2 8.5 - - + +
97B ILE* 1.3 76.3 - - - +
99B MET* 1.3 67.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 6.5 0.7 - - - -
50B VAL* 3.6 7.1 - - - +
51B ALA* 2.8 41.4 + - + +
53B LYS* 4.7 25.4 - - + +
70B GLU* 5.0 9.4 - - + +
71B ILE* 6.0 1.6 - - + -
74B LEU* 3.8 25.8 - - + -
83B THR* 5.9 4.9 - - - +
84B LYS 3.4 14.6 - - - +
85B TYR* 4.3 8.5 - - + -
86B TYR* 3.9 7.2 - - - -
97B ILE* 3.9 29.1 + - + +
98B ILE* 1.3 79.9 - - - +
100B GLU* 1.3 63.4 + - - +
101B TYR 3.4 0.2 + - - -
400B ATP 4.7 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL 5.7 0.2 - - - -
50B VAL* 5.3 0.2 - - - +
51B ALA 4.3 0.2 - - - -
82B VAL 4.0 0.9 - - - +
83B THR* 3.5 11.3 - - - -
84B LYS* 3.0 52.4 + - + +
86B TYR* 3.6 19.3 - - - +
99B MET* 1.3 71.7 - - - +
101B TYR* 1.3 64.7 + - - +
102B LEU* 3.8 15.6 + - + +
159B LYS* 2.7 35.1 + - - +
400B ATP 2.7 31.9 + - - -
----------------------------------------------------------
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