Contacts of the strand formed by residues 59 - 66 (chain B) in PDB entry 3QEK
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 GLN 59 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PRO* 4.8 10.3 - - + +
25B LYS 2.6 13.6 + - - +
26B ILE* 3.3 29.6 - - + +
27B VAL 2.8 26.2 + - - -
50B ASN* 3.9 11.0 - - - +
58B ILE* 1.3 73.6 - - - +
60B LEU* 1.3 72.8 + - - +
61B GLN* 3.3 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 3.4 33.4 - - + +
29B ILE* 4.5 15.7 - - + -
46B VAL* 3.7 17.4 - - + +
49B ALA* 4.1 14.6 - - + -
50B ASN* 2.8 37.0 + - - +
58B ILE* 5.3 2.2 - - + -
59B GLN* 1.3 75.5 - - - +
61B GLN* 1.3 67.7 + - - +
306B VAL* 5.5 2.7 - - + +
310B ALA* 3.5 36.1 - - + -
313B ILE* 4.2 15.3 - - + -
314B HIS* 4.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 3.8 21.9 - - + +
27B VAL 2.9 6.0 + - - +
28B ASN* 3.3 25.2 - - - +
29B ILE* 2.9 28.4 + - - +
46B VAL* 4.2 4.7 - - - -
59B GLN* 3.3 27.1 + - - -
60B LEU* 1.3 80.1 - - - +
62B ALA* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN* 4.7 0.2 + - - -
29B ILE 3.8 4.0 - - - -
42B PHE* 3.8 18.2 - - + -
43B ARG* 4.0 28.1 - - + +
46B VAL* 4.0 20.4 - - + +
61B GLN* 1.3 77.8 + - - +
63B THR* 1.3 66.2 + - - +
64B SER 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN* 3.0 29.1 + - - -
29B ILE 3.0 11.4 + - - -
30B GLY* 3.1 5.0 - - - -
31B ALA 3.0 22.0 + - - -
42B PHE* 3.8 1.8 - - - -
62B ALA* 1.3 71.9 + - - +
64B SER* 1.3 63.9 + - - +
81B ASP 3.4 24.7 - - - +
82B LEU* 3.8 9.7 - - + +
85B SER* 3.8 18.4 + - - +
87B VAL* 4.2 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 3.2 13.0 - - - -
33B LEU* 4.8 2.0 - - - -
39B GLU* 2.7 40.7 + - - +
42B PHE* 3.9 22.2 - - - -
43B ARG* 4.7 6.9 + - - +
62B ALA* 6.1 0.2 - - - +
63B THR* 1.3 80.2 - - - +
65B VAL* 1.3 71.8 + - - +
82B LEU* 4.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA 3.0 6.0 + - - +
32B VAL* 3.3 26.0 - - + -
33B LEU* 3.0 23.9 + - - +
39B GLU* 3.6 10.9 - - - +
64B SER* 1.3 81.0 - - - +
66B THR* 1.3 70.5 + - - +
68B ARG* 4.6 7.4 - - - +
74B MSE 4.2 4.0 - - + -
77B SER* 3.9 14.1 - - - +
81B ASP* 3.4 37.0 - - + +
82B LEU* 4.2 10.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
32B VAL* 4.2 3.1 - - - +
33B LEU 3.1 15.5 - - - +
34B SER 4.0 6.1 - - - -
35B THR* 3.7 27.8 - - - +
36B LYS* 4.0 6.1 + - + +
39B GLU* 3.6 23.7 + - + +
65B VAL* 1.3 85.6 - - - +
67B HIS* 1.3 68.0 + - - +
68B ARG* 3.5 28.3 + - - +
74B MSE 4.5 1.2 - - - +
----------------------------------------------------------
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