Contacts of the strand formed by residues 72 - 77 (chain B) in PDB entry 4I93
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 72 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 3.5 44.6 - - + -
63B SER* 3.6 5.4 - - - +
66B GLY 3.7 10.3 - - - +
67B GLU* 3.3 29.6 - - + +
69B ALA* 3.5 8.7 - - + +
70B PRO 5.0 0.4 - - - +
71B ASN* 1.3 80.1 - - - +
73B VAL* 1.3 64.0 + - - +
74B TYR* 3.9 18.6 - - + +
86B VAL 3.7 0.5 - - - +
87B LYS* 3.5 3.3 - - - +
88B ARG* 2.8 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 3.4 6.4 - - - +
62B VAL* 2.8 41.9 + - + -
63B SER* 3.0 24.0 + - - -
71B ASN 5.8 0.4 - - - +
72B VAL* 1.3 77.5 - - - +
74B TYR* 1.3 68.7 + - - +
85B ALA* 4.1 6.1 - - + -
86B VAL 3.2 15.5 - - - +
87B LYS* 4.1 14.4 - - + -
186B ARG* 6.4 0.2 - - - +
200B PHE* 4.0 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B THR* 4.2 11.9 - - + -
56B PHE* 3.4 55.6 + + + +
57B ALA 3.8 12.8 - - - -
60B ASN* 3.2 9.6 - - + +
61B ILE* 3.5 25.6 - - + -
62B VAL* 4.2 4.7 - - - -
67B GLU* 3.8 21.3 + - - +
72B VAL* 3.9 15.4 - - + +
73B VAL* 1.3 76.7 - - - +
75B LYS* 1.3 69.0 + - - +
85B ALA* 3.3 3.8 - - - -
86B VAL* 2.7 46.3 + - + +
88B ARG* 3.4 38.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B THR* 3.8 9.7 - - - +
59B GLU 4.3 10.9 + - - -
60B ASN* 2.8 57.7 + - - +
62B VAL* 3.9 21.4 - - + +
74B TYR* 1.3 74.3 - - - +
76B GLY* 1.3 60.8 + - - +
84B ILE 3.4 5.4 - - - +
85B ALA* 4.7 1.3 - - - +
134B PHE* 3.9 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA 3.1 17.0 - - - -
53B THR* 4.3 3.8 - - - -
60B ASN* 5.7 0.4 - - - -
75B LYS* 1.3 77.0 - - - +
77B LYS* 1.3 62.3 + - - +
83B ARG* 3.3 8.8 - - - +
84B ILE* 2.9 40.6 + - - +
86B VAL* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA* 3.0 29.1 + - - +
76B GLY* 1.3 75.3 - - - +
78B LEU* 1.3 71.2 + - - +
81B GLN* 2.9 53.5 + - - +
82B ARG 3.4 5.6 - - - +
83B ARG* 4.5 11.0 - - + -
84B ILE* 4.7 0.2 - - - -
----------------------------------------------------------
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