Contacts of the strand formed by residues 105 - 110 (chain C) in PDB entry 5I75
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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57C GLN* 3.8 0.2 - - - -
58C GLN* 2.9 42.5 + - + +
60C PRO* 5.4 8.3 - - + -
104C ALA* 1.3 75.4 - - - +
106C TYR* 1.3 65.1 + - - +
107C TYR* 3.6 35.5 - - + +
121C GLY* 4.3 3.6 - - - -
122C THR 3.9 22.0 - - - +
123C LYS* 4.1 27.1 - - + +
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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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26C GLN* 3.8 5.1 + - - -
41C ILE* 3.8 26.6 - - + +
55C TRP* 5.2 10.1 - + + -
56C TYR 3.4 13.0 - - - +
57C GLN* 4.1 16.8 + - + -
67C LEU* 3.9 17.3 - - + -
82C PHE* 4.0 7.6 - - - -
93C PHE* 3.5 32.5 - + - -
95C ILE* 3.5 18.7 - - + +
102C ASP* 3.0 26.6 + - - +
104C ALA* 3.4 22.4 - - + -
105C VAL* 1.3 73.7 - - - +
107C TYR* 1.3 61.5 + - - +
121C GLY* 3.4 4.7 - - - -
122C THR* 3.0 33.4 + - - +
124C LEU* 4.2 15.0 - - + -
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Residues in contact with TYR 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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58B GLN* 3.6 17.7 + - - -
62B LYS 3.8 8.9 + - - -
63B SER* 3.7 29.4 - - - -
64B LEU* 4.4 21.8 - - + -
26C GLN* 3.8 2.0 - - - -
54C ALA 3.7 0.3 - - - +
55C TRP* 3.4 9.0 - - - -
56C TYR* 2.9 46.2 + - + +
58C GLN* 3.2 28.8 + - + -
64C PRO* 5.8 0.2 - - + -
105C VAL* 3.6 35.7 - - + +
106C TYR* 1.3 75.0 - - - +
108C CYS* 1.3 62.5 + - - +
118C PHE* 4.8 5.6 - - + -
119C GLY 3.7 4.7 - - - -
120C GLY 3.8 5.1 + - - -
121C GLY* 3.7 22.7 - - - -
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Residues in contact with CYS 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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24C MET* 4.6 1.0 - - - +
26C GLN* 3.2 28.1 + - - -
43C CYS* 2.0 49.8 - - + -
53C VAL* 4.5 3.4 - - + -
54C ALA 3.3 6.5 - - - +
55C TRP* 3.7 22.7 - - + -
107C TYR* 1.3 74.8 - - - +
109C GLN* 1.3 62.1 + - - +
118C PHE* 3.4 2.9 - - - +
119C GLY* 2.7 34.8 + - - -
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Residues in contact with GLN 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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123B TYR 4.1 7.5 + - - +
125B PHE* 3.6 26.9 - - - -
24C MET* 4.6 5.1 - - - +
53C VAL* 3.5 2.8 - - - +
54C ALA* 2.9 37.4 + - - +
56C TYR* 3.3 33.4 + - + -
108C CYS* 1.3 76.5 - - - +
110C GLN* 1.3 76.1 + - - +
111C HIS* 3.5 12.4 + - - +
116C ARG* 4.7 7.0 - - + +
117C THR 3.2 18.2 - - - +
118C PHE* 3.4 29.2 - - + -
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Residues in contact with GLN 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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22C ILE* 3.5 24.1 - - + +
24C MET* 3.8 25.3 - - + +
49C VAL* 4.6 1.6 - - + -
52C ALA 3.4 9.4 - - - +
109C GLN* 1.3 87.2 - - - +
111C HIS* 1.3 57.5 + - - +
112C TYR* 3.1 43.6 + - + -
113C SER 3.4 9.9 + - - +
115C PRO 2.8 28.7 + - - -
116C ARG* 3.6 8.5 - - - +
117C THR* 3.3 26.7 + - - +
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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