Contacts of the strand formed by residues 134 - 140 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31Q VAL* 3.8 4.8 - - - +
78Q PHE* 3.8 20.4 - - + -
79Q SER 3.6 5.8 - - - +
80Q GLY 4.6 0.7 - - - -
81Q LEU 3.4 24.5 - - - +
84Q ASP* 3.5 19.1 - - + -
85Q SER* 3.7 11.2 - - - +
88Q LEU* 4.5 8.7 - - + -
120Q GLN* 3.1 14.0 + - - -
132Q PHE* 2.9 12.7 + - + -
133Q GLY* 1.3 84.0 - - - +
135Q SER* 1.3 73.4 + - - +
136Q THR* 3.8 13.0 - - + -
153Q PRO* 3.1 19.2 - - - +
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Residues in contact with SER 135 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Q LEU* 4.5 3.5 - - - +
31Q VAL* 3.5 25.1 - - - +
78Q PHE* 3.2 6.1 - - - +
79Q SER 3.1 27.7 + - - -
120Q GLN* 4.8 0.2 - - - +
134Q VAL* 1.3 71.7 - - - +
136Q THR* 1.3 65.3 + - - +
150Q GLN* 4.5 2.8 + - - -
151Q THR 3.2 14.6 + - - -
152Q GLU* 3.3 18.5 - - - +
153Q PRO* 3.5 5.7 - - - +
165Q ILE* 3.2 18.6 - - - +
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Residues in contact with THR 136 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q LEU* 4.1 22.0 - - + -
77Q SER 3.4 8.3 - - - +
78Q PHE* 4.2 6.3 - - + -
88Q LEU* 4.5 14.1 - - + -
116Q VAL* 4.7 1.9 - - + +
120Q GLN* 5.0 0.9 - - - +
134Q VAL* 3.8 16.4 - - + -
135Q SER* 1.3 82.1 - - - +
137Q LEU* 1.3 63.0 + - - +
138Q ILE* 3.7 11.5 - - - +
150Q GLN* 3.0 12.8 - - - +
151Q THR* 2.4 64.4 + - - +
165Q ILE* 4.1 1.6 - - - -
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Residues in contact with LEU 137 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q ALA* 4.1 8.5 - - + +
38Q VAL* 3.7 40.4 - - - +
39Q GLY* 3.8 6.3 - - - +
48Q LEU* 4.5 10.4 - - + +
75Q VAL 3.9 0.3 - - - +
76Q LEU* 3.3 3.8 - - - -
77Q SER* 2.9 50.5 + - - +
136Q THR* 1.3 81.6 - - - +
138Q ILE* 1.3 62.8 + - - +
139Q ALA 4.2 0.4 + - - -
148Q LEU* 4.7 7.9 - - + -
149Q TYR 3.2 11.2 - - - +
150Q GLN* 3.8 17.7 - - + -
163Q GLN* 4.1 20.9 - - + +
165Q ILE* 4.1 11.9 - - + -
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Residues in contact with ILE 138 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Q VAL* 3.8 24.7 - - + -
75Q VAL 3.4 4.5 - - - +
76Q LEU* 3.7 28.0 - - + -
109Q VAL* 3.8 10.4 - - + +
112Q LEU* 4.1 15.3 - - + -
113Q THR* 3.5 45.3 - - + +
116Q VAL* 4.3 9.4 - - + -
136Q THR* 3.7 17.0 - - - +
137Q LEU* 1.3 76.2 - - - +
139Q ALA* 1.3 63.3 + - - +
148Q LEU* 3.5 2.0 - - - +
149Q TYR* 2.8 35.0 + - + +
151Q THR* 4.3 2.0 - - + -
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Residues in contact with ALA 139 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Q VAL* 3.5 26.7 - - + -
48Q LEU* 4.3 12.5 - - + +
74Q VAL* 3.4 7.5 - - - +
75Q VAL* 2.9 45.1 + - + +
109Q VAL* 4.3 2.0 - - - -
137Q LEU 4.2 0.6 - - - -
138Q ILE* 1.3 75.2 - - - +
140Q GLY* 1.3 59.4 + - - +
147Q LYS 3.2 13.0 - - - +
148Q LEU* 4.1 7.9 - - + -
215Q VAL* 4.6 2.2 - - + -
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Residues in contact with GLY 140 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Q VAL* 4.6 1.8 - - - +
73Q HIS 3.3 13.5 - - - -
109Q VAL* 3.4 11.4 - - - +
139Q ALA* 1.3 77.7 - - - +
141Q PHE* 1.3 72.5 + - - -
147Q LYS* 3.0 33.3 + - - +
215Q VAL* 4.2 8.3 - - - -
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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