Contacts of the strand formed by residues 89 - 106 (chain C) 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 GLN 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B TYR* 3.4 38.4 + - - +
22B GLN* 3.8 23.1 - - + +
25B TYR* 3.6 50.1 - - + +
48C LYS* 4.1 7.1 - - - +
81C MET* 3.4 32.2 - - + +
82C ARG 3.8 2.9 - - - +
83C ILE* 3.6 27.3 - - + +
88C GLY* 1.3 69.4 - - - -
90C HIS* 1.3 58.8 + - - +
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Residues in contact with HIS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLN* 4.2 3.1 - - - -
81C MET* 4.4 0.9 - - - -
82C ARG* 2.9 41.6 + - + +
84C LYS* 3.3 28.5 + - - +
87C GLN* 3.0 38.7 + - + +
88C GLY 3.0 22.6 + - - -
89C GLN* 1.3 72.8 - - - +
91C ILE* 1.3 60.8 + - - +
92C GLY 3.3 4.7 + - - +
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Residues in contact with ILE 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 3.3 31.6 - - - -
22B GLN* 3.3 19.7 + - - +
79C GLN* 3.8 13.5 + - + +
80C ILE 3.7 22.9 - - - +
81C MET* 3.2 33.8 - - + -
90C HIS* 1.3 68.8 - - - +
92C GLY* 1.3 59.3 + - - +
93C GLU* 4.2 1.6 + - - +
17D PHE* 3.3 26.9 - - + -
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Residues in contact with GLY 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C MET 3.5 0.2 - - - +
79C GLN* 4.6 1.3 - - - -
80C ILE* 2.9 33.8 + - - +
82C ARG* 3.8 13.2 - - - +
90C HIS* 3.3 6.5 + - - +
91C ILE* 1.3 75.3 - - - +
93C GLU* 1.3 65.9 + - - -
94C MET* 3.7 5.5 + - - +
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Residues in contact with GLU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C THR* 3.8 17.8 - - + +
78C MET 3.2 8.3 - - - +
79C GLN* 4.7 11.0 + - + +
82C ARG* 5.4 1.0 + - - -
91C ILE 5.6 1.3 - - - +
92C GLY* 1.3 74.0 - - - -
94C MET* 1.3 62.3 + - - +
14D VAL* 3.6 32.9 - - + +
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Residues in contact with MET 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE* 4.1 6.5 - - + -
39C TYR* 4.0 23.8 - - + +
42C GLU* 3.6 14.6 - - - +
47C PHE* 3.1 29.4 - - + -
76C ILE 3.4 1.7 - - - +
77C THR* 3.3 6.6 - - - -
78C MET 2.8 34.1 + - - +
80C ILE* 3.3 36.1 - - + -
82C ARG* 3.7 19.7 - - - +
92C GLY 4.0 3.6 - - - +
93C GLU* 1.3 79.5 - - - +
95C SER* 1.3 62.3 + - - +
96C PHE* 3.8 21.8 + - + -
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Residues in contact with SER 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C TYR* 2.4 34.4 + - - -
75C ASN* 4.2 22.4 + - - +
76C ILE 3.3 7.2 + - - -
77C THR* 4.2 13.9 + - - +
94C MET* 1.3 73.8 - - - +
96C PHE* 1.3 60.1 + - - +
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Residues in contact with PHE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE* 3.6 42.0 - - + -
38C GLU* 3.8 24.7 - - + -
39C TYR* 3.5 19.7 - + - -
52C VAL* 3.8 29.2 - - + -
54C LEU* 3.6 22.2 - - + -
75C ASN* 3.2 7.9 - - - -
76C ILE* 2.9 34.7 + - + +
78C MET* 4.1 13.2 - - + -
80C ILE* 4.4 7.0 - - + -
94C MET* 3.8 35.0 - - + -
95C SER* 1.3 76.3 - - - +
97C LEU* 1.3 62.7 + - - +
98C GLN 3.5 0.5 + - - -
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C GLU* 3.9 10.8 + - - +
54C LEU* 3.8 4.2 - - - +
56C ARG* 2.7 48.0 + - - +
73C GLU* 3.6 37.2 - - + +
74C SER 3.8 7.6 - - - +
75C ASN* 3.5 19.8 - - - +
96C PHE* 1.3 71.7 - - - +
98C GLN* 1.3 72.1 + - - +
99C HIS* 4.6 7.0 - - + +
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Residues in contact with GLN 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PRO 4.8 3.2 + - - -
54C LEU* 4.2 6.5 - - + +
55C MET* 3.2 47.8 - - - +
73C GLU* 3.3 5.0 - - - -
74C SER* 2.7 46.1 + - - +
76C ILE* 3.5 46.7 - - + +
96C PHE 3.5 0.2 + - - -
97C LEU* 1.3 78.0 - - - +
99C HIS* 1.3 69.8 + - - +
100C ASN* 4.0 4.6 + - - +
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Residues in contact with HIS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PRO* 3.5 17.3 - - + +
55C MET* 2.9 22.0 + - - +
56C ARG* 3.4 33.9 + - + -
57C ALA* 2.9 30.1 + - + +
70C PRO* 3.5 40.9 - - + +
72C GLU 3.6 3.6 - - - -
73C GLU* 3.7 17.7 + - + -
97C LEU* 4.6 5.8 - - + +
98C GLN* 1.3 83.2 - - - +
100C ASN* 1.3 65.6 + - - +
101C LYS 4.4 5.6 - - - +
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Residues in contact with ASN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PRO* 3.7 8.7 - - - +
72C GLU* 2.6 38.0 + - + +
73C GLU 3.5 6.3 - - - -
74C SER* 2.7 36.9 + - - -
98C GLN* 4.5 5.4 + - - +
99C HIS* 1.3 75.5 - - - +
101C LYS* 1.3 66.4 + - + +
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Residues in contact with LYS 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PRO* 3.8 7.0 - - - -
70C PRO* 3.6 4.0 - - - +
71C THR* 2.9 32.6 + - - +
72C GLU* 3.3 40.5 + - + +
99C HIS* 4.4 2.0 - - - +
100C ASN* 1.3 87.1 + - + +
102C ALA* 1.3 63.5 + - - +
103C GLU* 6.0 0.4 - - - +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C CYS* 4.0 17.5 - - - +
27C HIS* 4.3 2.1 - - - -
28C PRO* 3.8 21.9 - - + +
57C ALA* 3.7 28.0 - - + -
69C VAL 3.3 13.9 - - - +
70C PRO* 4.2 0.2 - - + -
71C THR* 3.8 2.9 - - - -
99C HIS* 5.4 0.7 - - + -
101C LYS* 1.3 78.8 - - - +
103C GLU* 1.3 68.8 + - - +
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C TYR* 5.8 4.5 - - + +
26C CYS* 3.6 13.2 - - - -
69C VAL* 3.0 31.1 + - - +
71C THR* 3.5 26.1 + - + -
101C LYS* 6.0 0.5 - - - +
102C ALA* 1.3 76.0 - - - +
104C CYS* 1.3 67.2 + - - +
105C ARG* 2.9 32.9 + - - +
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Residues in contact with CYS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C TYR* 3.7 24.1 + - - +
26C CYS* 3.7 15.3 - - - -
61C CYS* 2.1 53.6 - - + -
66C LEU* 4.3 15.9 - - + +
67C GLU 3.6 5.2 - - - -
103C GLU* 1.3 77.3 - - - +
105C ARG* 1.3 68.0 + - - +
106C PRO* 4.9 0.2 - - - +
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Residues in contact with ARG 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LEU* 3.2 6.5 - - - -
67C GLU* 2.9 33.6 + - + +
69C VAL* 4.5 18.0 - - + +
70C PRO 5.5 0.2 + - - -
71C THR* 3.4 27.8 + - - +
103C GLU* 2.9 30.8 + - + +
104C CYS* 1.3 81.7 - - - +
106C PRO* 1.3 85.4 - - + +
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Residues in contact with PRO 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C GLY 3.4 10.3 - - - +
66C LEU* 3.5 11.7 - - + -
67C GLU* 4.3 3.6 - - - +
105C ARG* 1.3 97.0 - - + +
107C LYS* 1.3 70.7 + - - +
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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