Contacts of the strand formed by residues 122 - 127 (chain R) in PDB entry 3EPD
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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1681 LYS* 4.8 7.6 - - - +
66R TRP* 3.2 31.7 - - - -
67R ALA* 2.7 43.7 + - + +
68R ARG 5.2 0.7 - - - +
69R HIS* 4.9 15.5 - - + +
120R SER* 6.1 0.2 - - - -
121R TYR* 1.3 77.0 - - - +
123R CYS* 1.3 61.6 + - - +
124R LEU* 3.5 10.2 - - - +
135R VAL 4.6 0.2 - - - -
136R ASP* 3.5 32.8 - - + +
137R ILE* 4.3 2.0 - - - +
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Residues in contact with CYS 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49R CYS* 2.0 44.9 - - - -
51R LEU* 5.6 0.2 - - - +
64R LEU* 3.6 8.1 - - - -
65R THR 3.6 3.4 - - - -
66R TRP* 3.0 28.7 - - + +
122R THR* 1.3 79.0 - - - +
124R LEU* 1.3 59.5 + - - +
125R PHE* 3.6 12.1 - - - -
134R SER* 2.9 20.4 + - - -
135R VAL* 3.4 17.5 + - - +
137R ILE* 5.1 7.8 - - + +
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Residues in contact with LEU 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1651 PRO* 6.2 0.9 - - + -
1661 THR* 3.9 24.2 - - + +
1681 LYS* 4.4 16.6 - - - +
64R LEU* 3.3 0.6 - - - +
65R THR* 2.7 72.3 + - + +
67R ALA* 4.1 15.9 - - + +
122R THR* 3.5 24.2 - - - +
123R CYS* 1.3 72.7 - - - +
125R PHE* 1.3 65.3 + - - +
133R ARG 4.7 1.1 - - - -
134R SER* 3.6 12.3 - - - +
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Residues in contact with PHE 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1661 THR* 5.0 0.7 + - - -
49R CYS* 3.6 15.5 - - - -
51R LEU* 3.5 43.5 - - + -
59R THR* 6.3 1.6 - - + -
62R SER* 5.9 4.5 - - - -
63R GLN 3.6 8.5 - - - +
64R LEU* 3.5 25.6 - - + -
104R ARG* 3.4 42.4 - - + -
123R CYS* 3.6 15.5 - - - -
124R LEU* 1.3 78.9 - - - +
126R VAL* 1.3 68.1 + - - +
127R THR* 5.0 2.7 - - - +
131R GLY 3.0 15.3 - - - +
132R SER* 3.4 2.1 - - - -
133R ARG* 3.0 16.7 + - - +
134R SER* 2.9 26.9 + - - +
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Residues in contact with VAL 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091 ARG* 2.8 32.3 - - - +
1661 THR* 4.7 9.2 - - + -
2361 ASP* 4.6 4.5 - - - +
2401 VAL* 4.7 2.7 - - + -
59R THR* 4.4 1.2 - - - +
60R HIS 4.3 0.2 - - - -
61R VAL 4.5 0.4 - - - -
62R SER* 3.0 28.8 + - - +
63R GLN* 3.1 40.3 + - + +
65R THR* 5.3 3.1 - - - +
79R HIS* 4.9 4.5 - - + -
125R PHE* 1.3 79.5 - - - +
127R THR* 1.3 64.7 + - - +
131R GLY 3.5 1.8 - - - -
132R SER* 3.8 20.2 - - - +
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Residues in contact with THR 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071 MET 3.4 4.0 - - - +
1091 ARG* 3.8 9.7 + - - +
2401 VAL* 4.7 0.9 - - - +
59R THR* 3.4 31.4 + - + +
60R HIS 3.1 11.9 - - - +
61R VAL* 3.8 5.4 - - - +
125R PHE* 4.9 3.1 - - - +
126R VAL* 1.3 77.5 + - - +
128R PHE* 1.3 62.8 + - - +
129R PRO* 2.9 40.9 - - + +
130R GLN 4.3 3.1 - - - +
131R GLY* 3.0 30.2 + - - +
132R SER* 3.7 10.7 + - - +
133R ARG* 5.1 1.0 + - - -
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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