Contacts of the strand formed by residues 38 - 44 (chain M) in PDB entry 7K63
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 VAL 38 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30M MET* 3.3 32.5 - - + -
32M ALA* 3.9 16.8 - - + -
36M GLU* 4.0 0.7 - - + +
37M ARG* 1.3 81.7 - - - +
39M THR* 1.3 69.6 + - - +
40M ILE* 4.5 4.2 - - + +
92M LEU 3.8 0.2 - - - +
93M THR* 3.3 4.7 - - - +
94M ILE* 2.8 46.2 + - + +
97M LEU* 3.5 29.8 - - + -
123M LEU* 3.8 16.8 - - + -
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Residues in contact with THR 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M PRO* 4.5 3.1 - - - +
30M MET* 4.1 10.9 - - - +
37M ARG* 4.5 7.3 - - - +
38M VAL* 1.3 76.0 + - - +
40M ILE* 1.3 70.5 + - - +
41M THR* 4.2 15.5 + - - +
91M SER* 4.4 11.4 - - - -
92M LEU 3.1 10.3 - - - +
93M THR* 4.0 16.0 + - - +
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Residues in contact with ILE 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLN* 3.6 16.8 - - - +
27M PRO* 4.3 4.9 - - + -
30M MET* 4.1 12.6 - - + -
38M VAL* 4.5 5.8 - - + +
39M THR* 1.3 78.7 - - - +
41M THR* 1.3 65.4 + - - +
54M TRP* 3.8 10.6 - - + -
91M SER* 3.2 3.3 - - - -
92M LEU* 2.6 56.9 + - + +
94M ILE* 4.9 2.7 - - + -
105M TYR* 3.9 31.9 - - + -
121M THR* 3.6 36.6 - - + +
123M LEU* 4.4 11.4 - - + -
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Residues in contact with THR 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M THR 4.5 0.2 - - - -
25M GLN* 3.2 7.6 - - - +
26M SER* 3.0 42.3 + - - -
27M PRO* 3.9 7.6 - - - +
39M THR* 4.3 13.0 + - - +
40M ILE* 1.3 75.3 - - - +
42M CYS* 1.3 68.7 + - - +
43M LYS* 5.8 2.2 - - + -
54M TRP* 4.4 1.8 - - - -
89M ASP* 6.2 2.5 - - + -
90M PHE 3.6 9.9 - - - +
91M SER* 4.4 4.4 - - - +
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Residues in contact with CYS 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M MET* 3.5 23.1 - - - -
24M THR 3.5 8.7 - - - -
25M GLN* 4.7 0.4 - - + -
40M ILE 4.1 0.2 + - - -
41M THR* 1.3 80.1 - - - +
43M LYS* 1.3 65.8 + - - +
44M ALA 4.7 0.7 - - - -
52M LEU* 3.8 8.7 - - - -
54M TRP* 3.6 26.2 - - + -
88M GLN 4.4 0.2 - - - -
89M ASP* 3.7 2.8 - - - +
90M PHE* 2.8 44.7 + - + +
107M CYS* 3.4 28.3 - - - -
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Residues in contact with LYS 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M LYS 3.9 0.9 - - - +
23M MET* 3.7 1.7 - - - -
24M THR* 2.9 46.9 + - + +
41M THR* 5.8 2.7 - - + -
42M CYS* 1.3 76.8 - - - +
44M ALA* 1.3 72.2 + - - +
45M SER* 5.9 0.2 - - - -
88M GLN* 3.4 33.4 - - - +
89M ASP* 4.5 10.1 - - + +
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Residues in contact with ALA 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M ILE* 4.4 0.2 - - + -
22M LYS 4.0 3.1 - - - -
23M MET* 3.9 22.0 - - - -
42M CYS* 4.3 0.8 - - - -
43M LYS* 1.3 81.1 - - - +
45M SER* 1.3 66.0 + - - +
46M GLN 3.4 18.1 + - - +
48M ILE* 4.0 17.3 - - + -
88M GLN* 2.7 38.3 + - - +
90M PHE* 4.6 2.2 - - + -
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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