Contacts of the strand formed by residues 167 - 174 (chain A) in PDB entry 5T8Y
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 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ASP* 6.1 0.2 - - + -
74A ALA* 4.4 8.5 - - + -
75A LEU 3.3 6.1 - - - +
76A ALA* 3.7 18.4 - - + +
77A TYR* 3.2 10.4 + - - -
158A ILE* 4.2 5.2 - - + +
160A THR* 4.1 24.2 - - + +
163A TYR* 3.7 25.4 - - + -
164A GLY 4.2 0.7 - - - +
165A SER 2.7 18.2 + - - +
166A TYR* 1.3 79.3 - - - +
168A TYR* 1.3 62.1 + - - +
169A LEU* 4.3 9.4 - - + -
503A B12 2.5 46.9 + - - +
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Residues in contact with TYR 168 (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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74A ALA* 3.2 7.8 - - - -
75A LEU* 2.8 32.9 + - + +
77A TYR* 3.4 42.6 - + + +
98A ARG 3.4 6.9 + - - -
99A ALA* 3.3 37.5 + - + -
100A SER* 4.0 0.3 + - - -
101A TRP 4.5 8.5 + - - -
103A LYS 5.6 2.2 + - - -
105A TYR* 3.4 51.1 + + + +
109A LEU* 3.8 22.6 - - + +
167A VAL* 1.3 73.7 - - - +
169A LEU* 1.3 61.8 + - - +
261A MET* 3.8 28.0 - - + -
503A B12 3.9 9.0 - - + -
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Residues in contact with LEU 169 (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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73A ILE 3.7 4.0 - - - +
74A ALA* 3.8 19.7 - - + -
109A LEU* 3.4 7.6 - - - +
133A VAL* 5.9 0.9 - - - +
140A ASP* 3.8 27.7 - - + +
141A ARG* 4.2 1.1 - - - +
144A ALA* 3.7 24.0 - - + -
149A ILE* 4.1 13.9 - - + -
158A ILE* 3.8 13.7 - - + -
167A VAL* 4.3 4.7 - - + -
168A TYR* 1.3 83.6 - - - +
170A ALA* 1.3 64.6 + - - +
503A B12 3.0 71.1 + - + +
505A PO4 5.4 0.2 + - - -
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Residues in contact with ALA 170 (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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72A ALA* 3.4 3.6 - - - +
73A ILE* 2.9 47.2 + - + +
109A LEU* 3.6 22.6 - - + +
113A LEU* 4.2 12.6 - - + -
133A VAL* 4.7 10.3 - - + +
140A ASP* 5.1 1.3 - - - -
169A LEU* 1.3 78.2 - - - +
171A GLU* 1.3 73.2 + - - +
505A PO4 6.1 0.4 - - - -
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Residues in contact with GLU 171 (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 ILE* 3.8 11.4 - - + -
71A VAL 3.2 12.1 - - - +
72A ALA* 4.1 0.8 - - - +
113A LEU* 3.4 12.9 - - - +
132A MET* 3.1 54.5 + - + +
133A VAL 4.1 1.2 + - - +
138A LEU* 3.7 10.1 - - + +
140A ASP* 2.7 43.5 - - - +
143A VAL* 3.7 31.6 - - + +
170A ALA* 1.3 85.1 + - - +
172A MET* 1.3 62.4 + - - +
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Residues in contact with MET 172 (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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10A LEU* 5.1 3.1 - - + -
70A ILE* 4.2 0.9 - - - -
71A VAL* 2.8 60.3 + - + +
113A LEU* 3.8 16.2 - - + +
116A LEU* 4.2 30.5 - - + -
117A GLU* 3.6 34.1 - - - +
120A LEU* 4.2 10.8 - - + -
129A THR* 4.2 14.6 - - - -
130A LYS 4.0 6.3 - - - +
131A SER* 4.5 2.0 - - - +
171A GLU* 1.3 77.6 - - - +
173A ILE* 1.3 72.1 + - - +
174A THR* 3.5 15.2 + - + +
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Residues in contact with ILE 173 (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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27A ALA* 5.0 0.2 - - + -
60A PRO* 3.9 21.8 - - + +
63A LEU* 4.2 11.0 - - + -
64A LEU* 3.4 15.6 - - + +
67A ALA* 3.7 24.9 - - + -
69A SER 3.6 13.0 - - - +
70A ILE* 3.9 19.1 - - + -
129A THR* 3.2 5.9 - - - -
130A LYS* 3.0 33.3 + - + +
132A MET* 3.7 37.5 - - + -
138A LEU* 3.8 12.8 - - + -
172A MET* 1.3 72.3 - - - +
174A THR* 1.3 62.0 + - - +
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Residues in contact with THR 174 (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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64A LEU* 4.0 4.0 - - - -
67A ALA* 3.5 6.6 - - - +
68A LYS 3.3 13.5 + - - -
69A SER* 2.5 45.3 + - - +
71A VAL* 4.3 8.0 - - + +
120A LEU* 4.1 7.4 - - + -
128A ARG 3.5 8.7 - - - -
129A THR* 3.7 18.2 - - + -
172A MET* 3.7 26.5 - - + +
173A ILE* 1.3 78.6 - - - +
175A ASN* 1.3 59.5 + - - +
176A ILE* 3.3 21.5 + - + +
178A PHE* 4.2 3.2 - - + -
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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