Contacts of the strand formed by residues 79 - 84 (chain A) in PDB entry 1TQN
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 GLN 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A TYR* 3.2 4.1 - - - -
76A ASP* 2.9 40.5 + - + +
78A GLN* 1.3 77.0 - - - +
80A PRO* 1.3 101.1 + - - +
81A VAL* 3.5 2.7 + - + +
106A ARG* 4.1 18.4 - - - +
391A GLY 3.0 22.3 + - - +
393A VAL* 3.4 24.3 - - + +
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Residues in contact with PRO 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER* 4.3 8.5 - - - +
32A LEU* 3.7 31.0 - - + -
33A PHE* 3.8 11.9 - - + -
74A PHE 3.6 5.6 - - - +
75A TYR* 3.8 13.0 - - + -
78A GLN 3.3 10.3 - - - +
79A GLN* 1.3 103.2 + - - +
81A VAL* 1.3 62.5 + - - +
391A GLY 4.7 2.5 - - - +
392A VAL* 4.0 9.2 - - + -
393A VAL 3.0 21.9 + - - -
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.3 3.5 - - - -
73A GLY* 3.1 4.0 - - - -
74A PHE* 2.6 71.3 + - + +
76A ASP* 3.6 24.7 - - - +
79A GLN* 3.7 10.5 - - + +
80A PRO* 1.3 80.3 - - - +
82A LEU* 1.3 61.0 + - - +
106A ARG* 3.8 13.7 - - - +
393A VAL* 3.4 20.4 - - + +
395A MET* 3.7 22.2 - - + -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.9 8.3 - - + -
38A ILE* 3.8 18.8 - - + -
71A VAL* 3.1 29.2 - - + -
72A TRP 3.2 15.5 - - - +
81A VAL* 1.3 71.9 - - - +
83A ALA* 1.3 64.3 + - - +
84A ILE* 3.7 12.5 + - + -
386A MET* 4.0 10.3 - - + -
388A ILE* 3.3 38.4 - - + -
389A PRO* 6.2 1.1 - - + -
392A VAL* 3.8 17.2 - - + +
393A VAL 2.9 8.9 + - - +
394A VAL* 3.6 9.1 - - + +
395A MET 3.0 23.2 + - - +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS 4.8 0.2 - - - -
71A VAL* 3.5 7.4 - - - +
72A TRP* 2.7 75.7 + - + +
74A PHE* 4.6 1.5 - - + -
81A VAL* 3.9 2.6 + - - +
82A LEU* 1.3 73.1 - - - +
84A ILE* 1.3 63.9 + - - +
395A MET* 3.2 25.8 - - + +
397A PRO* 4.6 2.0 - - + -
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS 3.9 3.4 - - - -
71A VAL* 4.2 5.4 - - + -
82A LEU* 4.2 22.7 - - + +
83A ALA* 1.3 80.2 - - - +
85A THR* 1.3 64.8 + - - +
86A ASP 4.8 0.7 - - - +
89A MET* 3.6 34.1 - - + -
90A ILE* 3.9 38.0 - - + +
93A VAL* 4.1 7.9 - - + -
383A ILE* 5.4 2.0 - - + -
394A VAL* 3.7 21.8 - - + -
395A MET 2.9 15.0 + - - +
396A ILE* 3.9 13.6 - - + +
397A PRO* 3.3 19.2 - - - +
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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