Contacts of the strand formed by residues 122 - 127 (chain C) in PDB entry 5I73
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 THR 122 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C GLN* 2.9 17.4 + - - +
28C HIS 2.9 23.5 + - - +
29C LYS 3.5 4.9 - - - +
31C MET* 3.8 33.7 - - + +
41C ILE* 3.4 34.1 - - + +
104C ALA 4.0 0.7 - - - +
105C VAL* 3.8 1.9 - - - +
106C TYR* 3.0 33.2 + - - -
121C GLY* 1.3 69.6 - - - -
123C LYS* 1.3 61.7 + - - +
124C LEU* 3.2 8.0 + - - +
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Residues in contact with LYS 123 (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 LYS 3.1 7.7 + - - +
30C PHE* 3.8 37.8 - - + +
31C MET 3.5 16.3 + - - -
60C PRO* 6.0 5.2 - - - -
103C LEU* 6.0 5.8 - - + -
104C ALA 5.2 1.8 - - - +
105C VAL* 4.1 29.0 - - + +
121C GLY 4.0 1.6 + - - -
122C THR* 1.3 68.2 - - - +
124C LEU* 1.3 61.9 + - - +
125C GLU* 3.2 14.5 + - + +
185C ASP* 3.6 29.6 + - - +
186C GLN* 5.7 4.5 - - - +
193C TYR* 5.8 5.4 - - - -
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C MET* 3.5 25.6 - - + +
33C THR* 3.7 26.7 - - + -
39C VAL* 3.7 36.1 - - + -
41C ILE* 5.3 8.7 - - + -
95C ILE* 4.7 5.8 - - + -
98C VAL* 4.9 8.5 - - + -
102C ASP* 4.3 9.6 - - + +
103C LEU* 3.2 25.1 - - - +
104C ALA 3.5 17.5 + - - +
106C TYR* 4.0 26.0 - - + +
122C THR 3.2 5.3 + - - +
123C LYS* 1.3 70.0 - - - +
125C GLU* 1.3 58.4 + - - +
126C ILE* 4.4 3.2 - - + +
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Residues in contact with GLU 125 (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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30C PHE* 4.5 20.4 - - - +
31C MET 3.0 14.7 + - - +
32C SER* 2.8 23.4 + - - +
33C THR* 3.2 25.3 + - - +
103C LEU* 4.3 1.6 - - - -
123C LYS* 3.2 12.9 + - + +
124C LEU* 1.3 73.0 - - - +
126C ILE* 1.3 63.9 + - - +
160C TYR* 5.6 5.1 + - - +
186C GLN* 3.4 13.2 - - - +
193C TYR* 3.9 15.4 + - - +
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Residues in contact with ILE 126 (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 SER* 6.0 0.4 - - - -
33C THR* 3.2 9.9 - - + +
34C SER 4.6 1.1 - - - -
35C VAL* 4.3 22.9 - - + +
98C VAL* 4.5 12.6 - - + -
99C GLN 3.7 23.8 - - - +
100C ALA* 4.0 15.3 - - - +
102C ASP 5.0 0.4 - - - -
103C LEU* 4.2 23.1 - - + +
124C LEU* 4.4 4.7 - - + +
125C GLU* 1.3 74.9 - - - +
127C LYS* 1.3 69.9 + - - +
128C ARG* 4.0 1.5 + - + -
160C TYR* 2.9 14.9 + - - -
186C GLN* 2.6 35.8 + - - +
187C ASP 5.2 0.7 - - - +
191C SER* 3.7 23.7 - - - +
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Residues in contact with LYS 127 (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 SER* 5.0 9.0 - - - -
33C THR* 2.4 35.1 + - - +
34C SER* 3.3 34.4 + - - +
35C VAL* 4.1 2.4 + - - +
125C GLU 3.9 0.2 + - - -
126C ILE* 1.3 70.7 - - - +
128C ARG* 1.3 77.0 + - - +
130C ASP* 6.0 1.3 - - - -
160C TYR* 3.3 26.2 - - + +
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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