Contacts of the strand formed by residues 89 - 106 (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 GLN 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D LYS* 5.0 3.9 + - - +
81D MET* 3.2 32.1 - - + +
82D ARG 3.2 15.0 - - - +
83D ILE* 3.6 30.2 - - + +
88D GLY* 1.3 75.0 - - - +
90D HIS* 1.3 81.1 + - - +
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Residues in contact with HIS 90 (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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81D MET* 4.2 3.8 - - - -
82D ARG* 2.7 44.4 + - + +
87D GLN 4.7 4.5 + - - -
88D GLY* 4.4 7.0 - - - -
89D GLN* 1.3 104.4 + - - +
91D ILE* 1.3 65.7 + - - +
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Residues in contact with ILE 91 (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* 3.4 37.0 - - + -
79D GLN* 3.9 36.3 - - + +
80D ILE 3.5 6.7 - - - +
81D MET* 3.4 34.3 - - + -
90D HIS* 1.3 76.0 - - - +
92D GLY* 1.3 62.5 + - - +
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Residues in contact with GLY 92 (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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79D GLN* 3.4 4.2 - - - -
80D ILE* 2.7 42.4 + - - +
82D ARG* 5.5 6.0 - - - +
90D HIS 3.8 1.6 + - - -
91D ILE* 1.3 76.0 - - - +
93D GLU* 1.3 64.7 + - - -
94D MET* 4.5 2.5 - - - +
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Residues in contact with GLU 93 (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* 3.7 27.6 - - + +
77D THR* 3.5 25.1 - - + +
78D MET 3.4 4.9 - - - -
79D GLN* 4.9 11.1 + - + +
92D GLY* 1.3 75.5 - - - -
94D MET* 1.3 65.1 + - - +
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Residues in contact with MET 94 (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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35D ILE* 3.8 8.7 - - + -
39D TYR* 3.5 38.8 - - + +
42D GLU* 4.3 6.5 - - - +
47D PHE* 3.7 37.5 - - + -
76D ILE 3.7 0.7 - - - +
77D THR* 3.4 5.9 - - - -
78D MET* 2.9 32.0 + - - +
80D ILE* 3.7 28.9 - - + +
82D ARG* 5.0 11.0 - - - +
92D GLY 4.5 3.1 - - - +
93D GLU* 1.3 79.6 - - - +
95D SER* 1.3 62.4 + - - +
96D PHE* 3.9 19.5 - - + -
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Residues in contact with SER 95 (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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38D GLU* 5.8 0.2 - - - +
39D TYR* 2.5 35.7 + - - -
75D ASN* 4.6 18.6 - - - +
76D ILE 3.5 6.1 - - - -
77D THR* 4.0 12.2 + - - +
94D MET* 1.3 74.2 - - - +
96D PHE* 1.3 65.5 + - - +
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Residues in contact with PHE 96 (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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35D ILE* 3.9 36.1 - - + -
38D GLU* 4.2 19.5 - - + -
39D TYR* 3.4 25.8 - + - -
52D VAL* 3.9 30.7 - - + -
54D LEU* 3.8 22.0 - - + -
75D ASN* 3.3 6.9 + - - -
76D ILE* 2.9 36.5 + - - +
78D MET* 4.1 15.9 - - + -
80D ILE* 4.1 7.2 - - + -
94D MET* 3.9 32.1 - - + -
95D SER* 1.3 79.4 - - - +
97D LEU* 1.3 62.4 + - - +
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Residues in contact with LEU 97 (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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38D GLU* 4.6 4.4 + - - +
54D LEU* 4.0 4.0 - - - +
56D ARG* 2.4 51.1 + - - +
73D GLU* 3.8 39.5 - - + +
74D SER* 3.3 18.4 - - - +
75D ASN* 3.4 14.9 - - - +
96D PHE* 1.3 71.5 - - - +
98D GLN* 1.3 60.0 + - - +
99D HIS* 4.2 10.8 - - + +
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Residues in contact with GLN 98 (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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53D PRO 4.3 2.6 + - - -
54D LEU* 3.4 16.3 - - + +
55D MET* 2.8 48.0 - - + +
73D GLU* 3.6 4.0 - - - +
74D SER* 2.8 38.3 + - - +
75D ASN 5.5 0.2 - - - -
76D ILE* 3.2 48.3 - - + +
78D MET* 5.5 0.2 - - - +
96D PHE 3.5 0.2 + - - -
97D LEU* 1.3 75.1 - - - +
99D HIS* 1.3 75.0 + - - +
100D ASN* 4.0 3.4 + - - +
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Residues in contact with HIS 99 (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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28D PRO* 3.3 20.9 - - + +
55D MET* 2.8 21.2 + - - +
56D ARG* 3.6 26.6 + - + -
57D ALA* 3.0 31.7 + - + +
70D PRO* 3.4 43.4 - - + +
72D GLU 3.7 3.8 - - - +
73D GLU* 3.7 14.6 + - + -
97D LEU* 4.2 9.8 - - + +
98D GLN* 1.3 88.1 - - - +
100D ASN* 1.3 63.8 + - - +
101D LYS 3.4 5.6 - - - +
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Residues in contact with ASN 100 (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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28D PRO* 3.9 7.1 - - - +
72D GLU* 2.9 30.9 + - + +
73D GLU 3.1 20.0 - - - +
74D SER* 2.6 31.9 + - - -
98D GLN* 5.3 3.6 + - - +
99D HIS* 1.3 73.6 - - - +
101D LYS* 1.3 66.2 + - + +
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Residues in contact with LYS 101 (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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86A HIS* 3.7 33.2 + - + +
28D PRO* 3.9 8.5 - - - -
70D PRO* 3.8 2.9 - - - +
71D THR* 3.0 31.8 + - - +
72D GLU* 3.4 39.2 + - + +
99D HIS* 3.4 2.1 - - - +
100D ASN* 1.3 85.3 + - + +
102D ALA* 1.3 63.0 + - - +
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Residues in contact with ALA 102 (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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87A GLN 5.6 1.7 - - - +
26D CYS* 4.1 19.4 - - - +
27D HIS* 4.5 2.6 - - - -
28D PRO* 4.1 15.0 - - + +
57D ALA* 3.6 30.1 - - + -
69D VAL 3.3 16.8 - - - +
70D PRO* 4.0 0.7 - - + -
71D THR* 3.8 4.3 - - - -
99D HIS* 5.5 0.4 - - + -
101D LYS* 1.3 79.2 - - - +
103D GLU* 1.3 65.8 + - - +
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Residues in contact with GLU 103 (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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83A ILE* 6.6 0.2 - - + -
86A HIS* 3.8 27.2 + - - -
87A GLN 6.1 0.9 - - - +
25D TYR* 5.8 2.9 - - + -
26D CYS* 3.7 12.5 - - - -
67D GLU 3.5 0.5 - - - +
69D VAL* 3.1 25.1 + - - +
71D THR* 3.5 18.1 + - + +
102D ALA* 1.3 79.9 - - - +
104D CYS* 1.3 68.1 + - - +
105D ARG* 2.7 44.8 + - - +
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Residues in contact with CYS 104 (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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25D TYR* 3.3 29.8 + - - +
26D CYS* 3.9 8.5 - - - -
61D CYS* 2.0 50.7 - - - -
62D ASN 5.0 0.2 - - - -
66D LEU* 3.4 29.3 - - + +
67D GLU 3.1 5.4 - - - -
103D GLU* 1.3 81.3 - - - +
105D ARG* 1.3 67.7 + - - +
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Residues in contact with ARG 105 (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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86A HIS* 4.4 13.7 + - - -
66D LEU* 3.3 7.0 - - - -
67D GLU* 2.9 32.4 + - - +
69D VAL* 5.4 11.2 - - + -
71D THR* 4.2 19.3 - - + +
103D GLU* 2.7 43.1 + - + +
104D CYS* 1.3 86.1 - - - +
106D PRO* 1.3 78.7 - - + +
107D LYS 3.1 1.0 + - - -
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Residues in contact with PRO 106 (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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65D GLY 3.6 9.0 - - - +
66D LEU* 3.2 14.5 - - + -
67D GLU* 5.0 1.2 - - - +
105D ARG* 1.3 93.1 - - + +
107D LYS* 1.3 71.0 + - - +
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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