Contacts of the strand formed by residues 50 - 58 (chain C) in PDB entry 5D7A
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 LEU 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C VAL* 5.3 0.2 - - + -
41C LYS* 4.0 24.7 - - + +
42C GLY 3.3 14.1 - - - +
43C ARG* 3.9 28.5 - - - +
48C GLY 3.7 2.4 + - - +
49C GLN* 1.3 97.6 - - + +
51C ALA* 1.3 63.3 + - - +
86C TYR* 4.3 6.4 + - - -
107C PHE* 3.9 38.4 + - + +
163C GLU* 5.6 4.7 - - - +
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Residues in contact with ALA 51 (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 PHE* 3.8 31.2 - - + -
41C LYS* 3.6 1.7 - - - -
42C GLY* 2.6 38.0 + - - +
50C LEU* 1.3 79.0 - - - +
52C ALA* 1.3 59.2 + - - +
53C ILE* 3.9 1.5 - - + +
86C TYR* 3.8 11.9 - - + -
104C VAL* 3.8 7.9 - - + -
105C MET 3.5 11.2 - - - +
107C PHE* 3.5 12.0 - - - +
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 4.9 4.5 - - + -
40C TYR 3.3 7.2 - - - +
51C ALA* 1.3 70.7 - - - +
53C ILE* 1.3 60.8 + - - +
54C LYS* 5.7 0.4 - - - -
103C LEU 3.4 3.3 - - - +
104C VAL* 3.6 0.2 - - - -
105C MET* 2.7 42.7 + - - +
106C GLU 4.0 0.7 - - - +
107C PHE* 3.6 12.9 - - + +
401C 58C 3.4 48.7 - - + +
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Residues in contact with ILE 53 (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 PHE* 4.0 30.7 - - + -
26C GLU 4.0 3.1 - - - +
27C LEU* 3.8 26.7 - - + -
39C VAL* 3.3 2.5 - - - -
40C TYR* 2.5 46.8 + - - +
42C GLY* 3.8 17.5 - - - -
51C ALA 4.1 9.6 - - - +
52C ALA* 1.3 76.8 - - - +
54C LYS* 1.3 62.5 + - - +
55C VAL* 4.2 3.8 - - + -
102C TRP* 3.8 39.5 - - + -
103C LEU 3.5 4.9 - - - +
104C VAL* 4.3 12.8 - - + -
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Residues in contact with LYS 54 (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 THR* 2.9 44.6 + - - +
36C TYR* 6.0 0.6 - - - -
37C GLY 5.3 2.0 - - - +
38C GLN 3.5 4.9 - - - +
39C VAL* 3.7 23.6 - - + -
52C ALA 5.5 0.4 - - - +
53C ILE* 1.3 72.4 - - - +
55C VAL* 1.3 61.6 + - - +
56C MET* 3.8 24.6 + - + +
69C GLU* 3.2 25.0 + - - -
101C LEU 3.4 3.3 - - - +
103C LEU* 2.9 51.9 + - + +
105C MET* 5.0 12.9 - - + +
171C ASP* 3.6 16.6 + - - +
401C 58C 5.1 2.5 - - + -
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Residues in contact with VAL 55 (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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27C LEU* 4.6 4.7 - - + -
37C GLY* 3.5 3.6 - - - -
38C GLN* 2.8 43.8 + - - +
40C TYR* 3.6 31.4 - - + -
53C ILE* 4.2 6.1 - - + -
54C LYS* 1.3 71.7 - - - +
56C MET* 1.3 71.4 + - - +
57C ASP* 6.0 0.7 - - - +
100C GLN* 3.7 38.1 - - + +
101C LEU 3.2 7.9 - - - +
102C TRP* 3.8 27.4 - - + +
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Residues in contact with MET 56 (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 THR 4.5 1.3 - - - +
36C TYR* 3.5 26.7 - - - +
37C GLY* 4.8 1.3 - - - -
38C GLN* 5.9 0.9 - - - +
54C LYS* 3.8 36.3 - - + +
55C VAL* 1.3 83.2 - - - +
57C ASP* 1.3 67.6 + - - +
58C VAL* 5.8 0.4 - - + -
66C ILE* 4.7 11.4 - - + -
69C GLU* 3.9 19.7 - - - +
100C GLN* 3.4 4.9 - - - +
101C LEU* 2.8 64.1 + - + +
103C LEU* 4.5 7.9 - - + -
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Residues in contact with ASP 57 (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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36C TYR 5.2 0.4 + - - -
38C GLN* 5.0 9.0 + - - -
55C VAL* 6.0 0.9 - - - +
56C MET* 1.3 79.4 - - - +
58C VAL* 1.3 60.8 + - - +
59C THR* 5.1 1.5 - - + +
62C GLU* 3.1 15.3 - - - +
66C ILE* 5.3 1.4 - - - +
98C ASP* 3.4 32.9 - - - +
99C ASP 3.9 3.9 - - - +
100C GLN* 4.6 13.2 + - - +
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Residues in contact with VAL 58 (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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15C LEU* 5.9 2.5 - - + -
56C MET* 4.9 0.7 - - + -
57C ASP* 1.3 76.2 - - - +
59C THR* 1.3 77.8 + - - +
60C GLY* 5.5 0.2 - - - -
62C GLU* 3.7 2.0 - - - -
63C GLU* 5.4 4.0 - - + +
66C ILE* 3.7 23.8 - - + -
90C ILE* 5.4 12.6 - - + -
98C ASP* 3.2 20.7 - - - +
99C ASP* 2.9 33.0 + - + +
100C GLN 4.3 0.9 - - - -
101C LEU* 3.6 33.9 - - + +
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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