Contacts of the strand formed by residues 70 - 74 (chain B) in PDB entry 3AP3
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 LEU 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B MET* 3.4 26.8 + - + +
69B PRO* 1.3 76.7 - - - +
71B ILE* 1.3 60.2 - - - +
72B PHE* 4.5 13.5 - - + -
142B LEU* 4.7 8.3 - - + -
145B ILE* 4.3 20.6 - - + -
155B LEU* 3.4 32.5 - - + +
156B CYS* 5.1 0.9 - - - -
173B PHE* 3.6 44.2 - - + -
175B ASN 3.7 4.3 + - - +
176B SER* 3.9 11.9 - - - -
177B LYS* 2.6 37.1 + - - +
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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
----------------------------------------------------------
70B LEU* 1.3 77.6 - - - +
72B PHE* 1.3 74.6 + - - +
73B VAL* 4.4 5.2 - - + -
88B LEU* 4.5 7.2 - - + -
94B VAL* 3.6 23.3 - - + -
154B VAL* 3.7 20.0 - - + -
155B LEU 3.0 5.3 + - - -
156B CYS* 3.1 24.9 - - + +
157B ASN* 2.9 27.9 + - - +
177B LYS 3.5 4.5 - - - +
179B LEU* 4.3 22.9 - - + -
256B LEU* 4.1 34.5 - - + -
258B ILE* 4.4 3.8 - - + -
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Residues in contact with PHE 72 (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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70B LEU* 4.5 13.2 - - + -
71B ILE* 1.3 76.5 - - - +
73B VAL* 1.3 63.1 + - - +
103B ILE* 5.8 4.3 - - + -
141B ILE* 5.2 3.6 - - + -
145B ILE* 4.4 19.3 - - + -
157B ASN* 3.9 17.7 - - + -
162B THR* 4.9 9.6 - - + -
163B LEU* 4.1 7.2 - - + +
169B LEU* 3.8 31.9 - - + -
173B PHE* 4.1 23.3 - + - -
176B SER* 3.8 24.0 - - - -
177B LYS 2.7 9.6 + - - -
178B PHE* 3.2 41.9 - + + +
179B LEU* 2.8 28.8 + - - +
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Residues in contact with VAL 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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71B ILE* 4.4 3.6 - - + -
72B PHE* 1.3 77.9 - - - +
74B GLY* 1.3 62.4 + - - +
81B THR* 4.1 14.4 - - - +
84B MET* 4.1 22.0 - - + -
85B ARG* 4.4 3.1 - - + -
88B LEU* 3.8 21.1 - - + -
96B CYS* 4.4 2.2 - - - -
156B CYS* 3.7 18.2 - - - -
157B ASN* 3.0 21.9 + - - +
158B LYS* 3.7 20.9 - - + -
159B ASP 3.8 8.8 + - - -
162B THR* 3.3 15.8 + - - -
163B LEU* 3.5 2.4 - - - +
179B LEU* 3.8 11.2 - - + +
181B MET* 4.5 3.1 - - + -
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Residues in contact with GLY 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 VAL* 1.3 80.0 - - - +
75B GLY* 1.3 59.5 + - - -
81B THR* 3.5 16.3 - - - +
158B LYS* 5.4 0.4 - - - -
160B PRO* 3.5 18.4 - - - -
163B LEU* 3.5 15.4 - - - +
179B LEU 3.3 6.5 + - - +
180B LEU* 4.8 0.2 - - - -
181B MET* 3.2 23.4 + - - +
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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