Contacts of the strand formed by residues 81 - 87 (chain B) in PDB entry 5HAN
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 81 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 4.5 15.7 - - + -
28B TYR 3.6 16.4 - - - +
29B ILE* 4.2 12.1 - - + -
39B PHE* 3.3 8.5 - - - -
74B GLU* 4.5 11.2 - - + +
75B VAL* 3.3 4.7 - - - -
76B ASP* 2.9 51.2 + - + +
79B ASN* 4.1 10.5 - - + +
80B SER* 1.3 75.1 - - - +
82B MET* 1.3 66.7 + - - +
83B LYS* 4.3 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 3.6 1.0 - - - -
28B TYR* 2.8 60.6 + - + +
30B MET* 3.6 26.7 - - + -
39B PHE* 4.4 11.0 - - + -
43B ALA* 3.5 35.2 - - + -
46B PHE* 3.6 40.4 - - + -
72B VAL* 4.7 3.4 - - + -
74B GLU 3.7 4.3 - - - -
75B VAL* 4.5 1.8 - - + -
81B LEU* 1.3 75.0 - - - +
83B LYS* 1.3 63.3 + - - +
84B ILE* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 2.9 33.5 + - - +
26B CYS 3.3 4.3 - - - +
27B ALA* 4.1 22.7 - - + -
72B VAL* 3.6 5.0 - - - +
73B TYR* 3.0 45.6 + - + +
74B GLU* 2.8 49.7 + - + +
81B LEU* 4.3 19.6 - - + +
82B MET* 1.3 77.2 - - - +
84B ILE* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL 3.7 0.9 - - - +
25B LEU* 3.4 3.6 - - - -
26B CYS 2.9 31.3 + - - -
28B TYR* 3.8 16.4 - - + -
43B ALA 4.5 0.9 - - - +
46B PHE* 3.5 33.0 - - + -
47B ALA* 4.3 15.0 - - + +
70B ALA* 3.8 19.1 - - + -
71B LEU 3.4 11.2 - - - +
72B VAL* 4.1 10.3 - - + -
73B TYR* 3.6 4.5 - - - -
82B MET* 4.0 19.3 - - + -
83B LYS* 1.3 78.6 - - - +
85B ALA* 1.3 62.6 + - - +
86B TYR* 3.6 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 5.5 1.1 - - + -
17B LEU* 4.1 11.9 - - + -
23B HIS* 3.8 17.3 - - + -
24B VAL 3.5 4.7 - - - -
25B LEU* 3.7 18.8 - - + -
70B ALA* 3.2 4.5 - - - -
71B LEU* 2.9 43.4 + - + +
73B TYR* 3.6 12.7 - - + -
84B ILE* 1.3 71.4 - - - +
86B TYR* 1.3 60.8 + - - +
87B PRO* 3.7 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B HIS* 3.4 3.0 - - - -
24B VAL* 2.7 42.6 + - + +
26B CYS* 3.8 19.7 - - - -
28B TYR* 2.8 29.9 + - - -
50B SER* 3.3 45.7 + - - -
70B ALA* 3.7 15.9 - - + -
84B ILE* 3.6 32.9 - - + +
85B ALA* 1.3 72.7 - - - +
87B PRO* 1.4 70.6 - - + +
88B ILE* 3.2 0.5 + - - -
90B LEU* 4.3 8.3 - - + -
91B PHE* 3.7 23.3 - + + -
108B LEU* 4.4 3.6 - - + -
109B THR* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG 3.6 8.7 - - - +
23B HIS* 3.6 18.1 - - + +
67B GLY 4.4 6.1 - - - +
68B VAL* 3.6 30.5 - - + +
69B ASP 3.5 26.5 - - - +
71B LEU* 6.4 0.2 - - + -
85B ALA 3.7 4.9 - - - +
86B TYR* 1.4 82.4 - - - +
88B ILE* 1.3 64.8 + - - +
89B GLU* 3.1 14.8 - - - +
90B LEU* 3.1 28.3 + - + +
91B PHE* 3.9 2.8 - - - -
----------------------------------------------------------
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