Contacts of the strand formed by residues 66 - 79 (chain A) in PDB entry 1MKG
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 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 4.9 4.0 - - + +
61A CYS* 3.7 24.7 - - + +
63A ASP* 3.0 41.2 + - + +
65A GLY* 1.3 85.5 - - - +
67A GLU* 1.3 61.2 + - - +
104A CYS* 3.8 22.0 - - + +
105A ARG* 3.4 6.5 - - - +
106A PRO* 4.1 22.2 - - + -
107A LYS* 3.4 13.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A CYS* 3.5 7.0 - - - -
66A LEU* 1.3 74.5 - - - +
68A CYS* 1.3 60.1 + - - +
69A VAL* 3.6 26.3 + - + +
104A CYS* 3.3 1.0 - - - -
105A ARG* 2.9 39.7 + - - +
106A PRO 4.4 1.7 - - - +
107A LYS* 3.2 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A CYS* 2.0 52.5 - - + -
27A HIS 4.0 0.9 - - - -
57A ALA* 4.0 9.7 - - - +
58A GLY* 3.3 33.4 - - - -
59A GLY 4.0 13.5 - - - +
60A CYS* 5.3 0.2 - - - -
61A CYS* 3.6 6.4 - - - -
67A GLU* 1.3 67.9 - - - +
69A VAL* 1.3 65.4 + - - +
70A PRO* 4.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 4.2 1.6 - - - -
67A GLU* 3.6 37.5 - - + +
68A CYS* 1.3 80.1 - - - +
70A PRO* 1.3 97.9 - - + +
71A THR* 3.5 1.8 + - + +
102A ALA* 3.3 5.5 - - - -
103A GLU 3.2 33.5 + - - +
105A ARG* 5.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 4.2 3.8 - - + -
68A CYS 4.9 0.2 - - - +
69A VAL* 1.3 104.6 - - + +
71A THR* 1.3 61.7 + - - +
73A GLU* 3.8 21.5 - - + +
99A HIS* 3.5 48.9 - - + +
101A LYS 3.5 6.1 - - - +
102A ALA* 4.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 3.8 7.6 - - + +
70A PRO* 1.3 78.9 - - - +
72A GLU* 1.3 57.8 + - - +
73A GLU* 4.2 1.6 - - - -
101A LYS* 2.6 37.7 + - - +
102A ALA* 3.6 1.0 + - - -
103A GLU* 3.6 40.5 + - + +
105A ARG* 3.7 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PRO 3.9 0.2 - - - -
71A THR* 1.3 81.5 + - - +
73A GLU* 1.3 60.5 + - - +
99A HIS* 3.7 0.7 - - - -
100A ASN* 2.7 48.5 + - + +
101A LYS* 3.1 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PRO* 3.8 20.1 - - + +
71A THR 5.3 0.7 - - - -
72A GLU* 1.3 82.0 - - - +
74A SER* 1.3 69.2 + - - +
97A LEU* 3.7 32.6 - - + +
98A GLN 3.3 14.6 - - - +
99A HIS* 3.7 18.2 + - + -
100A ASN* 3.1 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 1.3 81.9 - - - +
75A ASN* 1.3 70.2 + - - +
97A LEU* 4.4 3.9 - - - +
98A GLN* 2.8 35.6 + - - +
100A ASN* 2.8 22.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 1.3 82.9 + - - +
76A ILE* 1.3 61.3 + - - +
77A THR* 5.3 1.3 + - - +
95A SER* 4.2 21.4 + - - +
96A PHE* 3.1 26.4 + - - +
97A LEU* 3.5 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PRO 5.6 0.2 - - - +
54A LEU* 4.0 16.2 - - + -
75A ASN* 1.3 75.8 - - - +
77A THR* 1.3 64.0 + - - +
78A MET* 4.1 12.7 + - + -
94A MET 3.5 0.9 - - - +
95A SER* 3.5 1.1 - - - -
96A PHE* 2.9 42.7 + - + +
98A GLN* 3.6 44.2 - - + +
15B VAL* 4.2 24.2 - - + -
23B ARG* 5.8 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN 5.3 1.2 - - - -
76A ILE* 1.3 76.5 - - - +
78A MET* 1.3 57.6 + - - +
93A GLU* 3.7 25.8 - - + +
94A MET 3.1 16.2 - - - +
95A SER* 3.6 12.5 + - - +
14B VAL* 3.1 31.0 - - + +
15B VAL* 2.7 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.8 30.1 - - - -
53A PRO* 3.8 32.1 - - + +
54A LEU* 4.7 3.6 - - + -
76A ILE* 4.2 17.0 - - + +
77A THR* 1.3 79.0 - - - +
79A GLN* 1.3 61.1 + - - +
80A ILE* 3.2 17.8 - - + +
92A GLY 3.2 2.9 - - - +
93A GLU* 3.2 1.2 - - - -
94A MET 2.9 31.6 + - - +
96A PHE* 4.3 11.7 - - + -
14B VAL* 3.9 5.4 - - - -
15B VAL* 3.4 32.8 - - + -
20B VAL* 3.8 19.1 - - + -
23B ARG* 4.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MET* 1.3 69.7 - - - +
80A ILE* 1.3 63.2 + - - +
91A ILE* 3.7 19.4 - - + +
92A GLY 3.2 5.6 - - - +
93A GLU* 4.6 12.4 + - + +
14B VAL* 4.1 12.6 - - + -
15B VAL 2.9 19.7 + - - +
16B LYS* 3.2 19.7 - - - +
17B PHE* 2.8 50.3 + - + +
20B VAL* 3.9 7.1 - - - +
18D MET* 3.9 25.8 - - - +
----------------------------------------------------------
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