Contacts of the strand formed by residues 78 - 95 (chain A) in PDB entry 1WQ9
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 SER 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET* 3.5 29.7 - - - +
70A ARG 3.1 11.4 - - - -
71A MET* 3.7 20.0 - - - -
76A HIS 5.0 1.0 + - - -
77A SER* 1.3 78.3 - - - +
79A LYS* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET* 4.2 6.3 - - - -
70A ARG* 3.0 46.1 + - - +
77A SER* 5.3 7.0 - - - +
78A SER* 1.3 78.1 - - - +
80A MET* 1.3 67.5 + - - +
81A GLU* 2.7 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 3.9 28.5 - - - +
68A ILE 3.4 7.9 - - - +
69A MET* 3.0 60.1 - - + +
79A LYS* 1.3 85.6 + - - +
81A GLU* 1.3 62.3 + - - +
5B PHE* 3.5 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 4.3 1.8 - - + -
67A GLN* 3.5 4.4 - - - +
68A ILE* 2.8 41.8 + - + +
70A ARG* 2.6 54.3 + - + -
79A LYS* 2.7 24.2 + - - +
80A MET* 1.3 78.3 - - - +
82A VAL* 1.3 71.1 + - - +
83A MET* 3.8 13.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 3.6 35.7 - - + +
66A ILE 3.5 4.0 - - - +
67A GLN* 5.1 8.1 - - + +
81A GLU* 1.3 80.7 - - - +
83A MET* 1.3 62.6 + - - +
84A LYS* 5.3 3.3 - - + +
2B VAL* 3.7 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.9 14.1 - - + -
27A HIS* 3.7 25.8 - - + +
30A GLU* 4.2 13.2 - - + +
35A PHE* 3.9 28.9 - - + -
65A ASP* 3.6 1.1 - - - -
66A ILE 2.8 32.4 + - - +
68A ILE* 3.9 17.7 - - + -
70A ARG* 4.1 7.0 - - - +
81A GLU* 3.8 16.1 + - + +
82A VAL* 1.3 76.1 - - - +
84A LYS* 1.3 62.3 + - - +
85A PHE* 3.5 38.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 2.8 34.1 + - + -
63A THR* 3.6 32.4 + - - +
64A ALA 3.3 6.1 - - - +
65A ASP* 3.0 26.5 - - - +
82A VAL* 5.3 3.6 - - + +
83A MET* 1.3 74.5 - - - +
85A PHE* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.5 1.3 - - + -
23A ILE* 3.8 14.1 - - + -
26A GLU* 3.9 28.5 - - + -
27A HIS* 3.9 13.9 - + - -
40A VAL* 3.7 20.6 - - + -
42A VAL* 4.0 18.6 - - + -
44A ARG* 5.3 1.3 - - - +
63A THR* 3.2 6.8 - - - -
64A ALA* 2.8 34.5 + - + +
66A ILE* 3.5 22.4 - - + -
68A ILE* 3.6 21.5 - - + -
83A MET* 3.5 47.8 - - + -
84A LYS* 1.3 78.7 - - - +
86A MET* 1.3 63.4 + - - +
87A GLU* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLU* 5.0 5.6 + - - +
42A VAL* 4.1 4.5 - - - +
44A ARG* 2.9 52.7 + - - +
61A LYS* 3.9 26.7 - - + +
62A HIS 3.6 8.1 - - - +
63A THR* 4.5 6.7 - - + +
85A PHE* 1.3 76.0 - - - +
87A GLU* 1.3 79.2 + - - +
88A HIS* 3.5 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.3 13.4 - - + -
43A LEU* 2.7 49.8 + - + +
61A LYS* 3.3 5.0 - - - -
62A HIS* 2.9 65.4 + - + +
64A ALA* 3.7 30.7 - - + +
85A PHE 4.4 1.3 - - - +
86A MET* 1.3 88.5 - - - +
88A HIS* 1.3 62.2 + - - +
3B ARG* 3.9 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.2 16.8 - - + +
43A LEU* 2.7 19.1 + - - +
44A ARG* 3.5 16.7 - - + -
45A CYS* 2.9 45.0 + - + +
58A PRO* 3.5 41.9 - - + +
60A GLY 3.6 2.0 - - - -
61A LYS* 4.0 8.9 - - + +
62A HIS* 3.7 8.6 - - - -
86A MET* 3.5 31.3 - - - +
87A GLU* 1.3 74.1 - - - +
89A THR* 1.3 60.8 + - - +
90A ALA 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.8 8.0 + - - +
60A GLY* 2.7 21.6 + - - -
61A LYS 3.2 19.8 + - - -
62A HIS* 2.9 27.8 + - + +
88A HIS* 1.3 74.1 - - - +
90A ALA* 1.3 62.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 4.0 5.8 - - - -
45A CYS* 3.4 2.3 - - - -
58A PRO* 3.3 6.8 - - - +
59A VAL* 2.8 39.6 + - + -
60A GLY* 3.8 4.2 + - - +
88A HIS 3.6 0.8 - - - -
89A THR* 1.3 83.3 - - + +
91A CYS* 1.3 66.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A CYS* 3.5 21.8 - - - +
15A GLN* 3.5 18.8 - - - -
16A THR* 3.4 17.0 - - - -
45A CYS* 2.0 46.7 - - + -
57A THR 3.0 8.3 - - - +
59A VAL* 3.9 6.9 - - - +
90A ALA* 1.3 78.6 - - - +
92A GLU* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A CYS* 4.0 6.9 - - - -
55A LYS 3.5 0.5 - - - +
57A THR* 2.9 31.1 + - - +
59A VAL* 3.4 14.8 - - + -
91A CYS* 1.3 78.6 - - - +
93A CYS* 1.3 74.1 + - - +
94A ARG* 2.4 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A CYS* 3.7 16.6 - - - -
49A CYS* 2.0 56.5 - - + -
50A THR 5.0 1.3 - - - -
54A MET* 3.8 17.7 - - + +
55A LYS 3.6 0.9 - - - -
92A GLU* 1.3 81.9 - - - +
94A ARG* 1.3 62.6 + - - +
95A PRO* 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MET* 3.5 5.6 - - - -
55A LYS* 2.7 38.3 + - + +
57A THR* 4.3 22.6 - - - +
58A PRO 4.5 9.4 + - - -
59A VAL* 3.4 25.0 - - - +
92A GLU* 2.4 40.2 + - + +
93A CYS* 1.3 79.0 - - - +
95A PRO* 1.3 75.1 - - + +
96A ALA* 3.3 1.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 3.5 6.5 - - - +
54A MET* 3.3 31.3 - - + -
94A ARG* 1.3 87.5 - - + +
96A ALA* 1.3 68.5 + - - +
----------------------------------------------------------
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