Contacts of the strand formed by residues 129 - 135 (chain C) in PDB entry 5L5E
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 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C VAL* 3.6 7.3 - - - +
73C PHE* 3.8 21.8 - - + -
74C SER 3.6 6.5 - - - +
75C GLY 4.8 0.4 - - - -
76C LEU 3.4 24.0 - - - +
79C ASP* 3.5 19.7 - - + -
80C SER* 3.8 9.2 - - - +
83C LEU* 4.2 14.8 - - + -
115C GLN* 2.9 24.1 + - - -
127C PHE* 3.0 6.7 + - + -
128C GLY* 1.3 83.9 - - - +
130C SER* 1.3 72.6 + - - +
131C THR* 3.9 14.1 - - + -
150C PRO* 3.4 9.5 - - - +
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Residues in contact with SER 130 (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 LEU* 4.4 3.8 - - - +
25C VAL* 3.5 23.3 - - - +
73C PHE* 3.3 3.1 - - - +
74C SER 3.0 31.6 + - - -
129C VAL* 1.3 71.7 - - - +
131C THR* 1.3 63.4 + - - +
147C GLN* 4.3 6.9 + - - -
148C THR 3.3 12.1 - - - -
149C GLU* 3.4 22.1 - - - +
150C PRO* 3.4 7.6 - - - +
162C ILE* 3.2 16.1 - - - +
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Residues in contact with THR 131 (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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71C LEU* 4.2 27.8 - - + -
72C SER 3.4 9.2 - - - +
73C PHE* 4.5 0.4 - - + -
83C LEU* 4.4 15.3 - - + -
111C VAL* 4.5 3.5 - - + +
115C GLN* 4.9 0.9 - - - +
129C VAL* 3.9 17.0 - - + -
130C SER* 1.3 77.4 - - - +
132C LEU* 1.3 62.4 + - - +
133C ILE* 3.7 11.3 - - - +
147C GLN* 3.3 10.7 - - - +
148C THR* 2.6 59.6 + - - +
162C ILE* 4.1 1.3 - - - -
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Residues in contact with LEU 132 (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 ALA* 4.0 9.0 - - + +
32C VAL* 3.7 18.2 - - - +
33C GLY* 3.7 26.9 - - - +
42C LEU* 4.5 6.1 - - + +
70C VAL 4.0 0.5 - - - +
71C LEU* 3.5 2.3 - - - -
72C SER* 2.8 50.0 + - - +
131C THR* 1.3 71.9 - - - +
133C ILE* 1.3 62.9 + - - +
134C ALA 4.2 0.5 + - - -
145C LEU* 4.6 14.1 - - + -
146C TYR 3.4 8.3 - - - +
147C GLN* 3.8 25.6 - - + -
157C TRP* 6.0 0.2 - - + -
160C GLN* 4.0 23.1 - - + +
162C ILE* 3.9 14.6 - - + +
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Residues in contact with ILE 133 (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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69C VAL* 3.8 18.2 - - + -
70C VAL 3.5 9.9 - - - +
71C LEU* 3.8 25.1 - - + -
104C VAL* 3.9 9.9 - - + +
107C LEU* 4.0 16.2 - - + -
108C THR* 3.6 45.1 - - + +
111C VAL* 4.3 7.0 - - + -
131C THR* 3.7 20.0 - - - +
132C LEU* 1.3 74.4 - - - +
134C ALA* 1.3 62.8 + - - +
145C LEU* 3.6 2.2 - - - -
146C TYR* 2.8 39.8 + - - +
148C THR* 4.2 4.9 - - + -
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Residues in contact with ALA 134 (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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40C VAL* 3.8 24.2 - - + -
42C LEU* 4.1 14.1 - - + -
69C VAL* 3.3 8.9 - - - +
70C VAL* 2.9 44.2 + - + +
104C VAL* 4.2 2.5 - - - -
132C LEU 4.2 0.6 + - - -
133C ILE* 1.3 74.6 - - - +
135C GLY* 1.3 59.3 + - - +
144C LYS 3.3 12.6 - - - +
145C LEU* 4.0 8.7 - - + -
213C VAL* 4.6 0.9 - - + -
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Residues in contact with GLY 135 (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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40C VAL* 4.6 2.1 - - - +
68C HIS 3.4 12.8 - - - -
104C VAL* 3.6 11.1 - - - +
134C ALA* 1.3 77.7 - - - +
136C PHE* 1.3 68.1 + - - -
144C LYS* 3.1 33.5 + - - +
213C VAL* 4.1 14.1 - - - +
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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