Contacts of the strand formed by residues 64 - 72 (chain B) in PDB entry 3I5D
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 LEU 64 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ARG* 5.8 2.9 + - - +
325A MET* 5.7 10.1 - - + -
327A PHE* 5.6 11.0 - - + -
62B THR 3.8 1.8 + - - -
63B VAL* 1.3 72.8 - - - +
65B SER* 1.3 59.5 + - - +
196B ILE* 3.3 5.9 - - - -
197B ARG* 2.8 49.6 + - + +
199B PRO* 4.5 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A MET* 4.2 15.6 - - - +
63B VAL* 3.8 5.4 + - - -
64B LEU* 1.3 75.6 - - - +
66B SER* 1.3 71.2 + - - +
67B VAL* 4.3 1.0 - - - +
194B ASN* 3.3 10.4 + - - -
195B ASN 4.0 2.9 - - - -
196B ILE* 3.7 2.9 - - - +
326B VAL* 3.1 46.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 5.2 3.1 - - - +
280A ARG* 6.2 0.2 - - - -
282A LEU* 3.8 26.5 - - - +
321A ARG* 4.5 0.7 + - - -
323A ASP* 2.9 25.3 + - - -
325A MET* 4.5 5.6 - - - -
65B SER* 1.3 79.8 + - - +
67B VAL* 1.3 63.9 + - - +
68B THR* 5.5 0.7 + - - -
193B LYS 4.1 0.3 - - - +
194B ASN* 2.9 15.9 + - - -
195B ASN* 3.1 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ARG* 2.8 25.8 + - - +
323A ASP* 5.0 0.8 + - - -
65B SER* 4.3 1.6 - - - +
66B SER* 1.3 79.4 + - - +
68B THR* 1.3 66.9 + - - +
69B THR* 5.4 0.9 - - + -
99B ASP 4.3 1.4 - - - +
100B GLY* 3.2 36.3 - - - +
192B ILE* 5.3 3.8 - - + -
193B LYS 3.3 6.3 - - - +
194B ASN* 3.6 20.4 - - + +
260B ILE* 5.2 0.4 - - + -
324B VAL* 3.7 34.1 - - + +
326B VAL* 3.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 4.7 8.7 - - - +
292A ALA* 6.6 0.4 - - + -
295A TYR* 4.0 27.2 - - + -
321A ARG* 3.2 13.1 + - - +
66B SER* 5.5 0.5 + - - -
67B VAL* 1.3 80.2 + - - +
69B THR* 1.3 72.2 + - - +
70B LYS* 5.9 0.9 - - + -
99B ASP 4.8 1.1 - - - -
191B LEU* 3.6 1.1 - - + +
192B ILE* 3.5 2.8 - - - -
193B LYS* 2.8 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TYR* 5.9 0.7 - - - -
67B VAL* 5.4 0.9 - - + -
68B THR* 1.3 88.3 - - - +
70B LYS* 1.3 63.2 + - - +
71B VAL* 5.4 0.6 - - - +
98B GLU 4.8 4.2 + - - -
99B ASP 4.3 6.2 + - - -
100B GLY 3.5 25.5 + - - +
102B PHE* 3.8 36.1 - - + +
190B VAL* 4.1 7.6 - - + -
191B LEU 3.2 8.1 - - - +
192B ILE* 4.5 7.6 - - + -
324B VAL* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA* 5.7 6.1 - - + -
296A ASN 5.8 3.8 - - - +
68B THR* 5.9 1.3 - - + -
69B THR* 1.3 76.3 - - - +
71B VAL* 1.3 64.8 + - - +
72B LYS* 3.8 2.4 + - - +
189B THR 3.9 0.3 - - - +
190B VAL* 3.7 0.5 - - - +
191B LEU* 2.9 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B THR* 5.6 0.9 - - - -
70B LYS* 1.3 75.0 - - - +
72B LYS* 1.3 63.8 + - - +
89B VAL* 3.7 36.6 - - + +
90B ALA* 4.5 13.5 - - - +
94B ILE* 3.5 18.3 - - + +
102B PHE* 3.6 37.9 - - + -
104B VAL* 4.7 5.4 - - + -
188B PHE* 4.4 9.9 - - + -
189B THR 3.4 8.7 - - - +
190B VAL* 3.7 14.1 - - + +
235B LEU* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LYS 3.8 2.6 + - - +
71B VAL* 1.3 75.2 - - - +
73B GLY* 1.3 58.8 + - - +
89B VAL* 3.7 3.8 - - - -
90B ALA* 6.2 0.4 - - - -
188B PHE* 3.7 2.4 - - - +
189B THR* 2.8 49.4 + - + +
----------------------------------------------------------
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