Contacts of the strand formed by residues 77 - 85 (chain A) in PDB entry 1TLY
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 PHE 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A TYR* 3.4 28.7 - + - -
54A ALA* 3.3 1.7 - - - -
55A ASP* 2.7 59.2 + - + +
76A LEU* 1.3 76.9 - - - +
78A MET* 1.3 68.9 + - - +
79A GLU* 4.3 4.0 - - - -
109A ILE* 3.6 30.5 - - + -
110A TYR 3.4 4.7 - - - -
111A ASP* 3.6 32.5 - - + +
120A GLN* 4.5 5.8 - - - -
152A TYR* 4.7 0.9 - - - -
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Residues in contact with MET 78 (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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53A TYR 3.2 11.4 - - - +
54A ALA* 4.0 17.0 - - + -
76A LEU* 4.8 11.9 - - + -
77A PHE* 1.3 79.7 - - - +
79A GLU* 1.3 61.4 + - - +
80A ILE* 4.2 22.7 - - + -
108A TYR* 5.4 8.1 - - + +
109A ILE* 3.7 2.9 - - - +
110A TYR* 2.8 61.1 + - + +
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Residues in contact with GLU 79 (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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51A TYR* 5.5 0.5 - - - -
52A GLY* 3.1 3.3 - - - -
53A TYR* 2.5 79.2 + - + +
77A PHE* 4.3 5.9 - - + -
78A MET* 1.3 75.5 - - - +
80A ILE* 1.3 64.5 + - - +
81A GLU* 4.5 10.7 - - + +
107A ASN* 3.3 28.0 + - - +
108A TYR 3.3 4.3 - - - +
109A ILE* 3.6 26.3 - - + +
164A ARG* 4.4 3.8 + - - -
166A LYS* 4.6 2.3 + - - -
188A ASN* 4.8 3.6 - - - +
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Residues in contact with ILE 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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50A PHE* 3.7 25.6 - - + -
51A TYR 3.6 2.9 - - - -
52A GLY* 4.4 1.8 - - - -
53A TYR 5.1 0.9 - - - +
78A MET* 4.2 22.9 - - + -
79A GLU* 1.3 80.2 - - - +
81A GLU* 1.3 62.4 + - - +
82A PRO* 3.5 16.2 - - + +
107A ASN* 3.5 4.5 - - - +
108A TYR* 2.8 67.4 + - + +
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Residues in contact with GLU 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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49A ASP* 4.0 1.2 - - - +
50A PHE* 3.7 3.9 - - - -
51A TYR* 2.6 51.2 + - + +
53A TYR* 6.1 0.5 - - - -
79A GLU* 4.5 9.9 - - + +
80A ILE* 1.3 72.9 - - - +
82A PRO* 1.3 63.8 - - - +
83A ARG* 3.8 8.2 + - + +
106A ASN 3.1 8.3 - - - +
107A ASN* 3.6 22.8 - - + +
144A TYR* 4.9 1.8 + - - +
166A LYS* 3.4 29.9 + - - +
168A LYS* 3.0 33.2 + - - -
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Residues in contact with PRO 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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48A PHE* 5.0 5.2 - - + -
49A ASP 3.9 4.9 - - - +
50A PHE* 4.0 15.5 - - + -
80A ILE* 3.5 26.0 - - + +
81A GLU* 1.3 88.9 - - - +
83A ARG* 1.3 59.8 + - - +
84A PHE* 4.4 20.0 - - + -
106A ASN* 2.9 50.7 + - + +
108A TYR* 5.2 0.7 - - + +
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Residues in contact with ARG 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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48A PHE* 3.3 9.6 - - - +
49A ASP* 2.9 65.3 + - - +
81A GLU* 4.3 7.6 - - + +
82A PRO* 1.3 79.9 - - - +
84A PHE* 1.3 63.6 + - - +
103A TYR* 3.6 30.8 - - + -
104A PHE 3.4 6.5 - - - +
105A ALA* 3.8 16.6 - - + -
106A ASN 4.4 1.3 - - - +
128A GLY* 4.3 0.2 - - - -
129A THR 3.8 21.2 + - - +
130A ASP* 3.4 22.6 + - - -
140A SER* 4.0 8.8 + - - -
142A ASN* 2.8 35.8 + - - +
144A TYR* 5.5 1.8 - - - +
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Residues in contact with PHE 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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47A TRP* 3.5 33.2 - + - +
48A PHE* 4.1 16.8 - + + -
82A PRO* 4.4 24.7 - - + -
83A ARG* 1.3 75.8 - - - +
85A SER* 1.3 63.9 + - - +
86A ILE* 4.3 0.2 - - - +
89A LEU* 4.0 16.6 - - + -
103A TYR* 3.1 7.0 - - - -
104A PHE* 2.7 69.1 + + + +
106A ASN* 4.3 12.6 - - - -
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Residues in contact with SER 85 (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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47A TRP* 2.8 24.9 + - - -
84A PHE* 1.3 69.7 - - - +
86A ILE* 1.3 62.8 + - - +
87A ASP 3.4 4.2 + - - -
88A LYS* 3.0 28.1 + - - +
89A LEU* 3.0 29.1 + - - +
101A GLU* 2.5 32.2 + - - +
102A TRP 3.6 5.6 - - - -
103A TYR* 3.7 7.9 - - - -
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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