Contacts of the strand formed by residues 134 - 140 (chain C) in PDB entry 3TDD
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 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C VAL* 3.8 5.5 - - - +
78C PHE* 3.8 20.0 - - + -
79C SER 3.6 7.0 - - - +
80C GLY 4.7 0.7 - - - -
81C LEU 3.4 25.1 - - - +
84C ASP* 3.5 17.9 - - + -
85C SER* 3.7 11.4 - - - +
88C LEU* 4.5 9.6 - - + -
120C GLN* 3.0 19.7 + - - -
132C PHE* 2.9 11.8 + - + -
133C GLY* 1.3 82.7 - - - +
135C SER* 1.3 76.5 + - - +
136C THR* 3.9 10.1 - - + -
153C PRO* 3.1 14.2 - - - +
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Residues in contact with SER 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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28C LEU* 4.5 3.3 - - - +
31C VAL* 3.5 25.1 - - - +
78C PHE* 3.2 6.4 - - - +
79C SER 3.1 27.2 + - - -
120C GLN* 4.7 0.2 - - - +
134C VAL* 1.3 70.6 - - - +
136C THR* 1.3 64.7 + - - +
150C GLN* 4.5 2.8 + - - -
151C THR 3.3 13.9 + - - -
152C GLU* 3.3 18.9 - - - +
153C PRO* 3.5 6.1 - - - +
165C ILE* 3.2 18.3 - - - +
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Residues in contact with THR 136 (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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76C LEU* 4.1 22.4 - - + -
77C SER 3.4 8.1 - - - +
78C PHE* 4.2 5.8 - - + -
88C LEU* 4.5 14.1 - - + -
116C VAL* 4.7 2.1 - - + +
120C GLN* 5.0 0.7 - - - +
134C VAL* 3.9 15.7 - - + -
135C SER* 1.3 81.0 - - - +
137C LEU* 1.3 63.7 + - - +
138C ILE* 3.7 15.9 - - - +
150C GLN* 3.1 12.0 - - - +
151C THR* 2.5 55.7 + - - +
165C ILE* 4.1 1.3 - - - -
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Residues in contact with LEU 137 (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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37C ALA* 4.1 8.7 - - + +
38C VAL* 3.7 40.4 - - - +
39C GLY* 3.8 6.1 - - - +
48C LEU* 4.5 10.5 - - + +
75C VAL 3.9 0.3 - - - +
76C LEU* 3.3 4.3 - - - -
77C SER* 2.9 48.9 + - - +
136C THR* 1.3 82.6 - - - +
138C ILE* 1.3 62.5 + - - +
139C ALA 4.2 0.4 + - - -
148C LEU* 4.7 7.6 - - + -
149C TYR 3.2 9.9 - - - +
150C GLN* 3.8 17.7 - - + -
163C GLN* 4.0 21.8 - - + +
165C ILE* 4.1 12.1 - - + -
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Residues in contact with ILE 138 (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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74C VAL* 3.8 24.0 - - + -
75C VAL 3.4 4.7 - - - +
76C LEU* 3.7 26.5 - - + -
109C VAL* 3.8 10.3 - - + +
112C LEU* 4.1 15.7 - - + -
113C THR* 3.5 45.8 - - + +
116C VAL* 4.3 7.4 - - + -
136C THR* 3.7 16.8 - - - +
137C LEU* 1.3 78.3 - - - +
139C ALA* 1.3 62.8 + - - +
148C LEU* 3.5 3.1 - - - -
149C TYR* 2.8 33.7 + - + +
151C THR* 4.4 3.8 - - + -
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Residues in contact with ALA 139 (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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46C VAL* 3.5 32.1 - - + -
48C LEU* 4.3 12.8 - - + +
74C VAL* 3.4 7.3 - - - +
75C VAL* 2.9 45.9 + - + +
109C VAL* 4.3 2.0 - - - -
137C LEU 4.2 0.4 + - - -
138C ILE* 1.3 75.2 - - - +
140C GLY* 1.3 58.7 + - - +
147C LYS 3.2 6.7 - - - +
148C LEU* 4.1 7.4 - - + -
215C VAL* 4.6 2.0 - - + -
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Residues in contact with GLY 140 (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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46C VAL* 4.5 2.3 - - - +
73C HIS 3.3 12.8 - - - -
109C VAL* 3.4 11.7 - - - +
139C ALA* 1.3 78.4 - - - +
141C PHE* 1.3 72.1 + - - -
146C PRO* 4.1 0.2 - - - +
147C LYS* 3.0 33.5 + - - +
215C VAL* 4.2 9.0 - - - -
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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