Contacts of the strand formed by residues 56 - 65 (chain B) in PDB entry 2QNJ
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 TYR 56 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B HIS* 3.1 8.4 - - - -
53B ILE* 2.8 46.1 + - + +
54B GLY 3.1 2.0 + - - -
55B ASN* 1.3 81.8 - - + +
57B ARG* 1.3 60.6 + - - +
58B LEU* 3.6 1.2 + - - +
73B ALA* 4.2 2.5 - - + -
74B ARG 3.4 1.8 - - - +
75B HIS* 3.2 42.8 + + + -
76B ILE* 4.4 1.1 - - - +
82B VAL* 3.7 20.9 - - + -
84B ILE* 3.7 20.4 - - + -
120B GLU* 2.5 41.6 + - - +
122B ILE* 4.0 9.9 - - + -
131B ILE* 3.6 35.8 - - + +
359B ALA* 3.7 9.9 - - - +
363B LEU* 3.9 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B MET* 2.9 39.4 + - - +
46B GLY* 5.0 2.0 - - - -
49B GLU* 3.5 28.0 + - + +
50B GLN* 2.9 43.1 + - + +
51B PRO 3.7 3.6 - - - -
52B HIS* 4.5 5.5 - - - +
56B TYR* 1.3 70.5 - - - +
58B LEU* 1.3 60.1 + - - +
59B LEU* 3.6 16.6 + - + +
73B ALA* 2.9 7.6 - - - -
74B ARG* 2.8 54.0 + - + +
76B ILE* 4.1 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLN* 3.5 24.3 - - - +
51B PRO* 2.9 34.3 + - + +
52B HIS 4.4 4.0 - - - -
53B ILE* 3.8 40.6 - - + +
56B TYR 4.3 1.1 - - - +
57B ARG* 1.3 71.4 - - - +
59B LEU* 1.3 62.3 + - - +
60B LYS 3.9 0.4 - - - -
71B LYS* 4.1 37.9 - - + +
72B LEU 3.9 1.8 - - - -
73B ALA* 4.1 4.5 - - + -
84B ILE* 3.8 21.1 - - + -
86B ILE* 5.0 7.0 - - + -
129B TYR* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLN* 2.9 38.6 + - - +
57B ARG* 4.0 22.4 - - + +
58B LEU* 1.3 76.2 - - - +
60B LYS* 1.3 71.0 + - + +
71B LYS* 5.2 0.2 - - - +
72B LEU* 2.7 40.3 + - + +
73B ALA* 4.2 10.3 - - - -
74B ARG* 4.3 13.2 - - + +
81B GLU* 4.5 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU 3.9 0.4 - - - -
59B LEU* 1.3 89.8 - - + +
61B THR* 1.3 67.2 + - - +
62B ILE* 3.4 23.1 + - - +
71B LYS* 3.4 8.7 - - - +
72B LEU* 3.0 43.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 1.3 77.5 + - - +
62B ILE* 1.3 62.3 + - - +
63B GLY 3.8 24.2 - - - +
64B LYS* 4.5 7.6 - - + +
69B LYS* 3.3 34.5 + - + +
70B VAL 3.6 6.3 - - - +
71B LYS* 3.4 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 3.6 37.5 - - - +
61B THR* 1.3 72.4 - - - +
63B GLY* 1.3 56.6 + - - +
70B VAL* 3.0 34.7 + - + +
72B LEU* 3.9 22.4 - - + +
83B ALA* 4.8 3.4 - - + -
134B TYR* 4.4 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 3.6 8.1 - - - +
62B ILE* 1.3 80.9 - - - +
64B LYS* 1.3 61.8 + - - +
69B LYS* 3.5 2.1 - - - -
70B VAL* 2.8 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 4.5 12.1 - - + +
63B GLY* 1.3 75.4 - - - +
65B GLY* 1.3 59.5 + - - +
68B ALA 3.8 5.2 - - - -
69B LYS* 4.6 10.5 - - + +
204B THR 5.0 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LYS* 1.3 77.0 - - - +
66B ASN* 1.3 71.7 + - - +
68B ALA 3.0 19.8 + - - +
204B THR 3.4 17.7 - - - +
208B LYS* 4.7 7.0 - - - -
----------------------------------------------------------
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