Contacts of the strand formed by residues 70 - 77 (chain B) in PDB entry 4AP8
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 ALA 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B CYS* 3.6 1.7 - - - +
69B GLY* 1.3 80.4 - - - +
71B ILE* 1.3 64.7 + - - +
140B SER* 3.2 5.0 - - - -
141B SER* 3.0 33.2 + - - +
143B HIS 4.0 1.3 - - - +
144B ARG* 3.5 41.3 - - + +
147B SER* 3.7 10.3 - - - +
1172B GOL 5.1 1.6 - - - +
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B SER* 4.4 9.9 - - - +
63B VAL* 3.9 27.1 - - + +
64B ILE* 4.1 30.5 - - + -
65B SER 5.7 0.2 - - - +
68B CYS* 5.7 2.2 - - + -
70B ALA* 1.3 79.7 - - - +
72B SER* 1.3 67.9 + - - +
73B LEU* 3.9 28.4 + - + +
138B ALA* 4.8 0.2 - - + -
139B VAL 3.3 7.0 - - - +
140B SER* 4.1 11.7 - - - -
147B SER* 4.3 0.2 - - - -
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Residues in contact with SER 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 1.3 75.5 + - - +
73B LEU* 1.3 62.8 + - - +
138B ALA* 3.4 3.3 - - - -
139B VAL 2.9 30.1 + - - +
147B SER* 2.8 40.2 + - - -
148B LEU* 3.3 29.3 + - - +
151B VAL* 3.5 12.4 - - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B VAL* 4.4 18.6 - - + -
60B SER* 4.2 27.4 - - - +
71B ILE* 3.9 21.5 - - + +
72B SER* 1.3 79.6 - - - +
74B PHE* 1.3 64.0 - - - +
75B VAL* 5.3 5.2 - - + -
136B ILE* 4.6 8.1 - - + -
137B ILE 3.2 6.5 - - - +
138B ALA* 3.8 20.9 - - + -
151B VAL* 4.2 6.9 - - - +
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 1.3 76.1 - - - +
75B VAL* 1.3 76.3 + - - +
76B GLY* 3.6 22.7 - - - -
135B ILE* 4.3 5.6 - - + -
136B ILE* 3.3 5.2 - - - +
137B ILE* 2.9 40.8 + - + +
151B VAL* 3.9 19.2 - - + +
155B ILE* 3.7 44.9 - - + -
159B LYS* 6.4 0.4 - - - -
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B VAL* 4.4 22.9 - - + -
73B LEU* 5.3 4.7 - - + -
74B PHE* 1.3 91.4 - - - +
76B GLY* 1.3 61.4 + - - +
77B THR* 3.7 18.9 + - + +
133B ALA* 3.7 27.8 - - + -
135B ILE 3.3 4.3 - - - +
136B ILE* 4.2 15.0 - - + -
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B PHE* 3.6 17.3 - - - -
75B VAL* 1.3 71.9 - - - +
77B THR* 1.3 56.3 + - - -
133B ALA* 3.2 6.1 - - - -
134B SER* 2.7 36.6 + - - -
135B ILE* 2.7 24.1 + - - -
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 3.7 23.7 + - + +
76B GLY* 1.3 78.8 - - - +
78B THR* 1.3 65.4 + - - +
79B ARG* 3.4 6.8 + - - +
90B LEU* 5.8 0.3 - - - +
92B TYR* 5.6 1.0 + - - -
131B SER* 4.4 15.9 - - - +
132B GLU 3.3 15.5 - - - +
133B ALA* 4.2 3.1 - - + +
134B SER* 4.7 4.4 + - - -
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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