Contacts of the strand formed by residues 27 - 34 (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 HIS 27 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C GLU* 5.8 1.6 - - - -
32C LEU* 4.2 13.8 - - + +
22D GLN 5.5 0.9 - - - -
23D ARG* 3.3 21.4 + - - -
25D TYR 3.0 25.1 - - - +
26D CYS* 1.3 76.5 - - - +
28D PRO* 1.3 86.0 + - + +
29D ILE* 3.4 24.5 + - + +
57D ALA* 4.2 3.1 - - - -
58D GLY* 2.8 36.1 + - - +
102D ALA* 4.5 7.9 - - - -
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Residues in contact with PRO 28 (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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27D HIS* 1.3 98.6 + - + +
29D ILE* 1.3 59.9 + - - +
55D MET* 3.5 27.6 - - + +
56D ARG 3.4 12.1 - - - +
57D ALA* 4.2 0.2 - - - -
99D HIS* 3.3 28.5 - - + +
100D ASN 3.9 15.9 - - - +
101D LYS* 3.9 14.6 - - - -
102D ALA* 4.1 9.4 - - + +
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Residues in contact with ILE 29 (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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29C ILE* 5.4 1.1 - - + -
30C GLU* 4.3 38.4 - - + +
32C LEU* 4.1 28.7 - - + +
27D HIS* 3.4 23.3 + - + +
28D PRO* 1.3 74.2 - - - +
30D GLU* 1.3 68.9 + - + +
31D THR* 2.7 34.4 + - - +
55D MET* 3.8 3.8 - - - -
56D ARG 2.8 28.7 + - - +
57D ALA 4.8 0.2 - - - -
58D GLY* 4.2 9.0 - - - -
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Residues in contact with GLU 30 (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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23C ARG* 3.0 35.3 + - - +
27C HIS* 5.7 3.8 - - - -
29C ILE* 3.7 34.2 - - + +
30C GLU 4.5 1.0 - - - +
29D ILE* 1.3 80.4 - - + +
31D THR* 1.3 63.1 + - - +
32D LEU* 5.5 3.7 - - + +
53D PRO* 3.7 25.4 - - + +
54D LEU 3.7 6.2 - - - +
55D MET* 3.5 20.5 - - - +
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Residues in contact with THR 31 (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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29C ILE* 6.4 0.4 - - - -
29D ILE* 2.7 29.8 + - - +
30D GLU* 1.3 74.8 + - - +
32D LEU* 1.3 70.9 + - - +
33D VAL* 3.4 16.8 + - + +
52D VAL 3.4 1.0 - - - +
53D PRO* 3.5 1.3 - - - +
54D LEU 2.7 41.2 + - - +
56D ARG* 3.8 16.5 - - + +
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Residues in contact with LEU 32 (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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23C ARG 4.2 3.8 - - - +
24C SER* 4.0 23.1 - - - +
27C HIS* 4.3 15.5 - - - +
29C ILE* 4.4 18.4 - - + +
58C GLY* 3.6 9.6 - - - +
59C GLY* 3.2 38.6 - - - +
30D GLU* 5.6 3.6 - - + +
31D THR* 1.3 78.7 - - - +
33D VAL* 1.3 61.2 + - - +
34D ASP* 4.2 2.8 + - - +
51D CYS* 4.4 7.6 - - - -
52D VAL 3.5 2.5 - - - -
53D PRO* 3.8 31.2 - - + -
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Residues in contact with VAL 33 (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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31D THR* 3.6 25.4 - - + +
32D LEU* 1.3 77.7 - - - +
34D ASP* 1.3 71.3 + - - +
35D ILE 3.4 0.7 + - - -
37D GLN* 3.6 15.7 - - - +
38D GLU* 3.4 33.0 - - + +
51D CYS* 3.1 3.8 - - - -
52D VAL* 2.8 40.4 + - + +
54D LEU* 3.9 24.5 - - + -
56D ARG* 4.2 14.6 - - + +
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Residues in contact with ASP 34 (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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60C CYS* 5.4 2.1 - - - +
32D LEU 4.2 2.8 + - - +
33D VAL* 1.3 76.1 - - - +
35D ILE* 1.3 66.0 + - - +
36D PHE* 3.1 48.6 - - + -
37D GLN* 2.9 25.3 + - + +
38D GLU* 3.6 7.7 + - - +
50D SER* 3.8 5.1 + - - +
51D CYS* 3.7 14.3 - - - +
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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