Contacts of the strand formed by residues 27 - 34 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLU* 5.6 4.9 + - - -
32A LEU* 4.3 11.5 - - + +
22B GLN 5.3 0.7 - - - -
23B ARG* 3.1 23.0 + - - -
25B TYR 2.9 24.2 + - - +
26B CYS* 1.3 74.7 - - - +
28B PRO* 1.3 90.8 + - + +
29B ILE* 3.3 29.9 + - + +
58B GLY* 2.8 32.3 + - - +
102B ALA* 3.9 5.2 - - - -
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Residues in contact with PRO 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B HIS* 1.3 99.3 + - + +
29B ILE* 1.3 58.0 + - - +
55B MET* 4.6 14.6 - - + +
56B ARG 3.4 13.0 - - - +
57B ALA* 4.2 0.7 - - - -
99B HIS* 3.5 23.8 - - + +
100B ASN 4.0 5.4 - - - +
101B LYS* 3.9 10.3 - - - -
102B ALA* 3.6 30.7 - - + +
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 6.0 0.9 - - + -
30A GLU* 4.8 28.0 - - + +
31A THR* 6.5 0.2 - - - -
32A LEU* 4.1 24.5 - - + +
27B HIS* 3.3 30.0 + - + +
28B PRO* 1.3 73.0 - - - +
30B GLU* 1.3 97.2 + - + +
31B THR* 2.9 24.8 + - - +
55B MET* 3.9 3.8 - - - -
56B ARG 2.8 29.0 + - - +
58B GLY* 4.6 4.9 - - - -
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ARG* 3.1 37.1 + - - +
27A HIS* 6.0 1.9 - - - -
29A ILE* 3.4 32.3 - - + +
30A GLU 4.5 3.5 - - - +
29B ILE* 1.3 90.2 - - + +
31B THR* 1.3 61.5 + - - +
32B LEU* 5.3 0.6 - - + +
53B PRO* 4.0 24.0 - - + +
54B LEU 3.7 3.6 - - - +
55B MET* 3.3 35.7 - - + +
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Residues in contact with THR 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 4.9 0.9 - - - -
29B ILE* 2.9 22.7 + - - +
30B GLU* 1.3 74.4 + - - +
32B LEU* 1.3 70.5 - - - +
33B VAL* 3.4 17.2 + - + +
53B PRO* 4.3 0.2 - - - -
54B LEU* 2.6 44.3 + - - +
56B ARG* 3.8 18.5 + - + +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ARG 4.1 4.3 - - - +
24A SER* 4.0 20.4 - - - +
27A HIS* 4.2 15.3 - - - +
29A ILE* 4.2 24.2 - - + +
58A GLY* 3.5 11.0 - - - +
59A GLY* 3.1 41.1 - - - +
30B GLU* 5.3 0.9 - - + +
31B THR* 1.3 76.9 - - - +
33B VAL* 1.3 62.0 + - - +
34B ASP 4.1 1.0 + - - -
51B CYS* 4.6 6.5 - - - -
52B VAL 3.7 1.6 - - - -
53B PRO* 3.7 29.4 - - + -
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B THR* 3.6 25.6 - - + +
32B LEU* 1.3 75.9 - - - +
34B ASP* 1.3 74.2 + - - +
35B ILE 3.3 0.7 + - - -
37B GLN* 3.6 17.7 - - - +
38B GLU* 3.4 30.7 - - + +
51B CYS* 3.0 3.0 - - - -
52B VAL* 2.7 43.3 + - + +
54B LEU* 3.8 23.1 - - + -
56B ARG* 4.4 11.9 - - + +
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Residues in contact with ASP 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU 4.1 1.2 + - - -
33B VAL* 1.3 79.5 - - - +
35B ILE* 1.3 64.0 + - - +
36B PHE* 3.0 35.7 + - - +
37B GLN* 2.9 29.7 + - + +
38B GLU 3.8 1.2 + - - -
50B SER* 3.4 15.2 - - - +
51B CYS* 3.9 6.2 - - + +
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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