Contacts of the strand formed by residues 63 - 71 (chain B) in PDB entry 3K5N
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 PHE 63 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN* 5.7 5.2 - - - -
57B LEU* 3.7 38.1 - - + -
60B GLU* 4.0 20.4 - - + -
61B GLN* 3.9 23.5 + - - +
62B GLY* 1.3 83.6 - - - +
64B ARG* 1.3 98.9 + - - +
65B LEU* 4.1 14.8 - - + -
81B LEU* 3.5 15.0 - - + -
82B TYR 3.0 16.8 - - - +
83B CYS* 3.6 15.9 - - - +
88B GLN* 4.1 0.7 - - - +
92B TYR* 3.6 21.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLU* 2.6 39.1 + - - -
63B PHE* 1.3 92.5 - - - +
65B LEU* 1.3 61.8 + - - +
66B THR* 3.2 22.2 + - - +
80B GLY 3.4 0.2 - - - +
81B LEU* 3.3 3.8 - - - -
82B TYR* 2.7 63.6 + - + +
84B ARG* 4.1 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.9 17.7 - - + -
50B VAL* 4.4 7.9 - - + -
53B ALA* 4.3 20.2 - - + -
54B GLN* 4.0 26.9 - - + +
57B LEU* 5.1 1.3 - - + -
63B PHE* 4.1 18.4 - - + -
64B ARG* 1.3 75.9 - - - +
66B THR* 1.3 63.8 + - - +
67B PRO* 4.3 3.6 - - - +
79B TYR* 4.3 27.8 - - + -
80B GLY 3.5 3.1 - - - +
81B LEU* 3.8 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 3.2 32.3 + - - +
65B LEU* 1.3 75.2 + - - +
67B PRO* 1.3 80.9 - - + +
68B LEU* 3.2 14.0 - - + +
79B TYR* 3.0 6.1 - - - -
80B GLY 2.7 40.5 + - - -
82B TYR* 4.1 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU 4.3 2.2 - - - +
66B THR* 1.3 90.3 - - + +
68B LEU* 1.3 71.2 + - - +
78B VAL 4.2 0.2 - - - +
79B TYR* 3.4 44.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 4.5 13.9 - - + -
66B THR* 3.2 16.6 - - + +
67B PRO* 1.3 82.9 - - - +
69B ALA* 1.3 59.8 + - - +
70B LEU* 3.1 27.5 + - + +
77B PRO* 5.3 4.2 - - - +
78B VAL* 3.2 20.4 + - + +
79B TYR 3.4 2.0 - - - -
80B GLY* 2.6 47.1 - - - +
82B TYR* 4.2 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 1.3 74.2 - - - +
70B LEU* 1.3 66.0 - - - +
71B LYS* 4.8 6.2 + - - -
385B GLY* 4.7 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 4.0 19.1 - - + -
68B LEU* 3.1 14.5 - - + +
69B ALA* 1.3 84.6 - - - +
71B LYS* 1.3 64.2 + - - +
77B PRO* 3.9 2.9 - - - +
78B VAL* 3.2 30.8 + - + +
382B HIS* 3.7 40.6 - - + +
385B GLY* 3.6 17.3 - - - +
386B TYR 4.3 0.7 - - - +
387B VAL* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA 4.8 6.7 + - - -
70B LEU* 1.3 76.7 - - - +
72B ASP* 1.3 63.5 + - - +
75B ARG* 3.9 28.5 - - + +
76B GLN 3.3 16.4 - - - +
77B PRO* 4.0 4.9 - - + -
78B VAL* 4.2 5.4 - - - +
384B ALA 5.0 0.8 + - - -
385B GLY* 3.0 25.8 + - - +
386B TYR* 3.2 37.0 - - + +
387B VAL* 3.2 21.2 + - - -
440B GLU* 5.5 0.2 - - - -
463B LYS* 5.8 2.0 - - - +
----------------------------------------------------------
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