Contacts of the strand formed by residues 105 - 110 (chain C) in PDB entry 5DPW
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 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C ILE* 4.3 5.4 - - + -
28C PRO 3.0 15.2 + - - +
29C VAL* 3.5 26.2 - - + +
30C VAL* 2.9 24.8 + - - +
79C VAL* 5.8 1.6 - - + -
91C MET* 4.7 9.0 - - + -
94C ILE* 4.2 10.1 - - + +
95C TYR* 3.8 43.3 - - + +
98C TYR* 4.1 18.4 - - + +
99C LYS* 4.2 2.0 - - - -
104C PHE* 1.3 74.4 - - - +
106C TYR* 1.3 61.5 + - - +
107C MET* 4.8 5.4 - - + -
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Residues in contact with TYR 106 (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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3C PHE* 3.8 9.8 - + + -
4C LYS* 3.7 23.4 - - + +
12C ARG* 3.5 17.8 + - - -
30C VAL* 3.6 33.7 - - + -
32C GLU* 4.3 11.4 - - - +
79C VAL* 3.5 7.2 - - - +
80C ASN* 2.6 50.4 + - - +
98C TYR 5.1 0.4 + - - -
100C ASP* 3.3 37.5 - - + -
102C ASP* 2.5 32.1 + - - -
104C PHE* 3.7 14.8 - - + -
105C VAL* 1.3 75.0 - - - +
107C MET* 1.3 58.8 + - - +
108C THR* 5.2 0.9 - - - +
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Residues in contact with MET 107 (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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29C VAL* 4.0 12.6 - - + -
30C VAL 2.8 16.2 + - - +
31C VAL* 4.3 5.2 - - + -
32C GLU* 2.9 27.5 + - - +
56C MET* 3.5 30.5 - - + -
59C PHE* 3.4 29.4 - - + -
77C LEU* 3.8 23.3 - - + -
78C LEU 3.3 10.1 - - - +
79C VAL* 4.4 14.8 - - + -
91C MET* 3.6 25.4 - - + -
94C ILE* 4.4 8.1 - - + -
105C VAL* 4.8 4.0 - - + +
106C TYR* 1.3 78.3 - - - +
108C THR* 1.3 66.3 + - - +
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Residues in contact with THR 108 (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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32C GLU* 3.2 18.1 + - + +
33C ARG 3.5 4.5 - - - +
34C TYR* 3.3 33.2 - - + +
35C PRO* 4.5 1.3 - - + -
77C LEU* 4.3 2.2 - - - -
78C LEU* 2.8 41.9 + - - +
80C ASN* 4.6 0.7 - - - -
81C ASN* 3.5 46.6 + - - +
106C TYR* 5.2 0.9 - - - +
107C MET* 1.3 78.0 + - - +
109C TYR* 1.3 59.6 + - - +
110C ALA* 5.3 0.2 - - - -
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Residues in contact with TYR 109 (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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31C VAL* 3.6 15.0 - - + -
32C GLU* 2.9 38.6 + - - -
33C ARG* 3.4 29.5 + - + +
34C TYR* 3.2 18.8 + - - +
37C GLU* 4.7 0.9 - - - +
40C LEU* 3.8 19.0 - - + +
41C PRO 3.7 14.4 - - - -
42C PRO* 3.3 7.8 - - - +
43C LEU* 3.0 53.8 + - + +
63C ILE* 4.7 2.5 - - + -
67C MET* 4.1 11.7 - - + -
75C PHE* 3.4 23.8 - + + -
76C TYR 3.3 4.9 - - - +
77C LEU* 4.1 9.3 - - + +
108C THR* 1.3 70.8 - - - +
110C ALA* 1.3 61.7 + - - +
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Residues in contact with ALA 110 (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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34C TYR* 3.6 30.7 - - + -
37C GLU* 3.8 5.4 - - - -
40C LEU* 4.1 6.1 - - - -
75C PHE* 4.4 0.6 - - - -
76C TYR* 2.8 38.3 + - + +
78C LEU* 4.3 16.6 - - + -
108C THR 3.9 0.6 + - - +
109C TYR* 1.3 76.8 - - - +
111C SER* 1.3 59.4 + - - +
112C GLN* 4.2 8.5 - - - +
113C GLU* 4.6 5.6 - - + +
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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