Contacts of the strand formed by residues 69 - 76 (chain A) in PDB entry 5D0A
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 SER 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PHE* 5.8 0.4 - - - -
25A THR 3.3 14.6 - - - -
26A THR* 4.8 0.2 - - - -
27A ALA* 3.7 4.8 - - - +
68A LYS* 1.3 79.6 - - - +
70A ILE* 1.3 70.1 + - - +
71A VAL* 4.9 0.2 - - - +
173A ILE* 3.4 5.9 - - - +
174A THR* 2.6 56.1 + - - +
176A ILE 2.7 18.2 + - - -
178A PHE* 3.4 27.3 - - - -
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Residues in contact with ILE 70 (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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24A PHE* 3.6 4.3 - - - +
25A THR* 2.8 40.8 + - + +
26A THR 3.5 17.3 - - - +
27A ALA* 4.3 3.8 - - - -
30A PHE* 4.0 19.5 - - + -
60A PRO* 3.7 26.2 - - + -
69A SER* 1.3 82.0 - - - +
71A VAL* 1.3 66.0 + - - +
72A ALA 3.8 0.5 + - - -
138A LEU* 4.4 5.4 - - + -
143A VAL* 3.7 26.7 - - + -
171A GLU* 3.8 17.0 - - + -
172A MET 3.4 12.8 - - - +
173A ILE* 4.2 13.0 - - + +
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Residues in contact with VAL 71 (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* 4.0 15.5 - - + -
22A ILE* 3.6 33.9 - - + -
23A GLY 3.5 5.2 - - - +
24A PHE* 3.6 25.1 - - + -
69A SER* 4.9 0.2 - - - +
70A ILE* 1.3 74.6 - - - +
72A ALA* 1.3 60.5 + - - +
73A ILE* 4.4 8.3 - - + +
113A LEU* 5.2 0.4 - - + +
116A LEU* 5.0 2.7 - - + -
171A GLU* 3.0 5.0 - - - -
172A MET* 2.7 62.1 + - + +
174A THR* 4.6 4.0 - - + -
178A PHE* 4.3 12.3 - - + -
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Residues in contact with ALA 72 (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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22A ILE* 3.2 6.1 - - - +
23A GLY 2.8 33.9 + - - +
70A ILE 3.8 1.4 + - - -
71A VAL* 1.3 72.3 - - - +
73A ILE* 1.3 63.8 + - - +
143A VAL* 4.0 16.8 - - + -
144A ALA* 4.3 7.0 - - + -
147A ALA* 3.9 18.6 - - + -
149A ILE* 3.7 22.7 - - + +
170A ALA 3.6 7.0 - - - +
171A GLU* 4.1 1.6 - - - +
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Residues in contact with ILE 73 (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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19A VAL* 3.7 25.4 - - + -
21A LYS 3.3 4.3 - - - -
22A ILE* 4.3 9.6 - - + -
71A VAL* 4.4 4.9 - - + +
72A ALA* 1.3 81.0 - - - +
74A ALA* 1.3 62.7 + - - +
75A LEU* 4.2 18.6 - - + -
109A LEU* 4.3 6.3 - - + +
112A LYS* 4.3 11.2 - - + -
113A LEU* 3.9 27.1 - - + +
116A LEU* 3.8 25.4 - - + -
144A ALA* 6.1 0.2 - - - +
149A ILE* 4.7 2.4 - - - +
169A LEU* 3.5 5.7 - - - +
170A ALA* 2.9 52.5 + - + +
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Residues in contact with ALA 74 (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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19A VAL* 3.8 0.2 - - - +
20A ASP* 2.9 25.1 + - - +
21A LYS* 2.8 23.0 + - + +
73A ILE* 1.3 76.4 - - - +
75A LEU* 1.3 66.5 + - - +
76A ALA 4.3 0.2 - - - -
149A ILE* 3.9 26.0 - - + -
160A THR* 5.5 0.2 - - + -
163A TYR* 6.5 0.2 - - + -
167A VAL* 4.2 13.7 - - + -
168A TYR 3.2 10.5 - - - +
169A LEU* 3.9 7.6 - - + -
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Residues in contact with LEU 75 (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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18A GLY 3.7 13.7 - - - +
19A VAL* 4.0 21.5 - - + -
20A ASP* 3.3 4.5 - - - +
73A ILE* 4.2 8.5 - - + -
74A ALA* 1.3 81.2 - - - +
76A ALA* 1.3 63.3 + - - +
77A TYR 3.6 0.7 + - - -
108A VAL* 4.2 16.6 - - + -
109A LEU* 4.1 24.2 - - + -
112A LYS* 4.5 11.2 - - + -
167A VAL* 3.2 4.2 - - - -
168A TYR* 2.9 35.1 + - - +
258A HIS* 3.6 25.8 - - + +
261A MET* 4.0 20.9 - - + -
505A PO4 4.4 3.1 - - - +
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Residues in contact with ALA 76 (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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20A ASP* 2.7 17.8 + - - +
75A LEU* 1.3 71.4 - - - +
77A TYR* 1.3 61.2 + - - +
78A PRO* 4.7 0.5 - - - +
163A TYR* 3.5 41.1 - - + -
166A TYR 3.4 8.7 - - - +
167A VAL* 3.9 2.8 - - - +
255A PHE* 4.0 20.9 - - + +
257A LEU* 4.6 2.4 - - + +
258A HIS* 3.2 25.5 - - - -
261A MET* 3.8 0.9 - - - +
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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