Contacts of the strand formed by residues 66 - 83 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ILE* 5.6 10.1 - - + -
64B GLU* 6.2 2.2 - - + -
25D TYR* 5.5 2.0 - - - +
61D CYS* 3.9 9.0 - - + +
63D ASP* 2.8 42.3 + - + +
64D GLU* 3.8 0.9 - - - +
65D GLY* 1.3 81.4 - - - +
67D GLU* 1.3 62.0 - - - +
104D CYS* 3.4 31.6 - - + +
105D ARG* 3.2 8.1 - - - +
106D PRO* 3.2 37.0 - - + -
107D LYS* 3.2 16.9 - - - -
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D CYS* 3.4 10.3 - - - -
66D LEU* 1.3 76.8 - - - +
68D CYS* 1.3 62.0 + - - +
69D VAL* 3.8 23.2 - - + +
103D GLU 3.5 0.9 - - - +
104D CYS* 3.1 2.1 - - - -
105D ARG 2.9 34.5 + - - +
106D PRO 5.0 0.9 - - - +
107D LYS* 3.8 37.2 - - + +
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Residues in contact with CYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D CYS* 2.0 52.0 - - + -
27D HIS 4.1 0.7 - - - -
57D ALA* 4.1 10.9 - - - +
58D GLY* 3.5 29.8 - - - -
59D GLY 3.6 16.2 - - - +
60D CYS* 5.3 0.2 - - - -
61D CYS* 3.4 5.6 - - - -
67D GLU* 1.3 71.4 - - - +
69D VAL* 1.3 72.8 + - - +
70D PRO* 4.9 0.3 - - - +
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Residues in contact with VAL 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ALA* 4.2 2.0 - - - -
67D GLU* 3.8 31.6 - - + +
68D CYS* 1.3 88.8 - - - +
70D PRO* 1.3 92.8 - - + +
71D THR* 3.4 3.9 - - + +
102D ALA* 3.3 5.2 - - - +
103D GLU 3.1 31.5 + - - +
105D ARG* 5.4 10.5 - - + -
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Residues in contact with PRO 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ALA* 4.0 5.5 - - + -
68D CYS 4.9 0.2 - - - +
69D VAL* 1.3 103.9 - - + +
71D THR* 1.3 61.4 + - - +
73D GLU* 3.8 18.4 - - + +
99D HIS* 3.4 50.5 - - + +
101D LYS 3.8 7.2 - - - +
102D ALA* 4.0 4.7 - - + -
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Residues in contact with THR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D VAL* 3.4 11.9 - - + +
70D PRO* 1.3 79.1 - - - +
72D GLU* 1.3 65.4 + - - +
73D GLU* 4.4 2.4 + - - -
101D LYS* 3.0 26.1 + - - +
102D ALA* 3.7 0.9 + - - -
103D GLU* 3.5 38.2 + - + +
105D ARG* 4.2 21.5 - - + +
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Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D THR* 1.3 81.9 + - - +
73D GLU* 1.3 69.1 + - - +
99D HIS* 3.7 2.9 - - - +
100D ASN* 2.9 45.1 + - + +
101D LYS* 3.4 50.7 + - + +
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Residues in contact with GLU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D PRO* 3.8 17.8 - - + +
71D THR 5.1 1.8 - - - -
72D GLU* 1.3 84.0 - - - +
74D SER* 1.3 67.1 + - - +
97D LEU* 3.8 23.8 - - + +
98D GLN 3.6 7.4 - - - +
99D HIS* 3.7 27.8 + - + -
100D ASN* 3.1 6.8 - - - +
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Residues in contact with SER 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D GLU* 1.3 79.6 - - - +
75D ASN* 1.3 72.1 + - - +
97D LEU* 3.3 3.7 - - - +
98D GLN* 2.8 34.0 + - - +
100D ASN* 2.6 34.3 + - - -
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Residues in contact with ASN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D SER* 1.3 85.7 + - - +
76D ILE* 1.3 61.5 + - - +
77D THR* 4.3 1.4 + - - +
95D SER* 4.6 19.1 - - - +
96D PHE 3.3 15.3 + - - +
97D LEU* 3.4 22.5 - - - +
98D GLN* 5.3 0.7 - - - -
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Residues in contact with ILE 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL* 6.0 0.7 - - - +
15C VAL* 3.7 29.4 - - + -
23C ARG* 5.7 2.2 - - - +
54D LEU* 4.0 14.6 - - + -
75D ASN* 1.3 75.5 - - - +
77D THR* 1.3 66.1 + - - +
78D MET* 4.3 9.9 - - + -
94D MET 3.7 0.9 - - - +
95D SER* 3.5 2.9 - - - -
96D PHE* 2.9 34.9 + - + +
98D GLN* 3.2 46.4 - - + +
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Residues in contact with THR 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL* 3.1 23.9 - - + +
15C VAL* 2.8 34.0 + - - +
75D ASN* 5.2 2.1 + - - +
76D ILE* 1.3 79.0 - - - +
78D MET* 1.3 58.2 + - - +
93D GLU* 3.5 41.1 - - + +
94D MET 3.4 11.0 - - - +
95D SER* 4.0 10.6 + - - +
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Residues in contact with MET 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL* 4.5 1.8 - - - -
15C VAL* 3.4 35.0 - - + +
20C VAL* 4.0 12.8 - - + -
23C ARG* 4.6 4.9 - - - +
52D VAL* 3.8 27.8 - - - -
53D PRO* 3.3 36.6 - - + +
54D LEU* 4.0 9.4 - - + -
76D ILE* 4.3 13.9 - - + +
77D THR* 1.3 75.3 - - - +
79D GLN* 1.3 64.2 + - - +
80D ILE* 3.4 15.4 + - + +
93D GLU* 3.4 3.1 - - - -
94D MET 2.9 30.2 + - - +
96D PHE* 4.1 15.0 - - + -
98D GLN* 5.5 0.2 - - - +
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Residues in contact with GLN 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C VAL* 4.0 16.1 - - + +
15C VAL 3.0 14.5 + - - +
16C LYS* 3.4 13.7 - - - +
17C PHE* 2.8 56.6 + - + +
20C VAL* 4.1 4.5 - - - +
78D MET* 1.3 71.8 - - - +
80D ILE* 1.3 67.4 + - - +
91D ILE* 3.9 17.2 - - + +
92D GLY 3.4 6.3 - - - -
93D GLU* 4.5 11.3 + - + +
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Residues in contact with ILE 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C PHE* 4.3 1.1 - - - -
20C VAL* 4.0 12.8 - - + -
35D ILE* 3.6 20.6 - - + -
47D PHE* 4.1 4.3 - - + -
48D LYS 3.8 8.7 - - - +
49D PRO* 3.9 8.3 - - + +
52D VAL* 3.8 26.5 - - + -
78D MET* 3.7 15.3 - - + +
79D GLN* 1.3 87.1 - - - +
81D MET* 1.3 75.9 + - - +
82D ARG* 3.4 3.6 + - - +
91D ILE* 4.2 1.8 - - - -
92D GLY 2.7 35.3 + - - +
94D MET* 3.7 27.9 - - - +
96D PHE* 4.1 10.5 - - + -
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Residues in contact with MET 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C PHE* 3.6 18.2 - - + -
46D ILE 4.0 0.2 - - - +
47D PHE* 3.5 4.7 - - - -
48D LYS* 3.1 57.7 + - + +
80D ILE* 1.3 76.2 - - - +
82D ARG* 1.3 60.9 + - - +
83D ILE* 4.0 15.5 - - + -
89D GLN* 3.2 42.6 - - + +
90D HIS* 3.4 9.2 - - - +
91D ILE* 3.4 32.5 - - + +
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Residues in contact with ARG 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D GLU* 2.6 34.2 + - - -
45D TYR* 3.1 48.0 - - + -
46D ILE 3.8 2.9 - - - -
47D PHE* 3.9 21.7 - - + -
80D ILE 3.4 3.9 + - - +
81D MET* 1.3 75.4 - - - +
83D ILE* 1.3 61.6 + - - +
84D LYS* 4.0 0.9 + - - +
89D GLN* 3.2 21.3 - - - -
90D HIS* 2.7 29.8 + - + +
92D GLY* 5.5 6.1 - - - +
94D MET* 5.0 12.0 - - - +
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Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D TYR* 3.3 8.9 - - - -
46D ILE* 2.7 67.4 + - + +
48D LYS* 3.8 37.5 - - + +
81D MET* 4.0 7.4 - - + -
82D ARG* 1.3 77.8 - - - +
84D LYS* 1.3 67.2 + - - +
85D PRO* 3.4 9.0 - - + +
88D GLY 4.0 9.2 - - - +
89D GLN* 3.6 29.2 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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