Contacts of the strand formed by residues 80 - 85 (chain B) in PDB entry 3ANX
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 ARG 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 1.3 80.0 + - + +
81B VAL* 1.3 61.6 + - - +
102B GLU* 3.3 31.3 + - - +
103B LYS* 3.2 27.1 - - + +
150B GLU* 5.0 9.6 - - - +
151B ARG* 3.4 27.6 - - - +
152B TYR* 3.4 17.1 - - + +
153B ASP* 2.9 39.7 + - - +
154B VAL 3.4 4.5 + - - -
186B ASN* 5.2 3.4 - - - +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET* 4.0 24.7 - - + -
78B PRO* 5.0 3.4 - - + -
80B ARG* 1.3 81.4 - - - +
82B LEU* 1.3 77.1 + - - +
83B ILE* 3.9 14.3 + - + -
95B VAL* 4.2 19.1 - - + -
101B VAL* 4.4 11.9 - - + -
103B LYS 2.8 8.9 + - - +
104B ALA* 3.3 11.5 - - + -
105B VAL 3.0 26.3 + - - +
152B TYR* 3.9 6.5 - - - -
154B VAL* 3.2 26.7 - - + +
156B ILE* 4.6 2.7 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 1.3 82.0 - - - +
83B ILE* 1.3 58.3 + - - +
84B VAL* 3.8 16.2 - - + -
105B VAL* 3.4 24.0 - - + +
107B VAL* 3.6 26.0 - - + -
144B TYR* 4.9 4.9 - - + -
145B LEU* 4.0 28.0 - - + -
152B TYR* 3.9 36.9 - - + +
154B VAL 2.8 6.9 + - - -
155B VAL* 3.3 25.0 - - + -
156B ILE* 2.7 30.4 + - - -
181B VAL* 5.2 0.7 - - + -
184B HIS* 5.7 2.0 - - + -
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Residues in contact with ILE 83 (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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81B VAL* 4.0 12.8 - - + +
82B LEU* 1.3 79.0 - - - +
84B VAL* 1.3 60.9 + - - +
85B GLY 3.6 17.7 - - - +
91B THR* 3.7 29.6 - - + +
92B LEU* 3.3 51.8 - - + +
95B VAL* 4.4 12.3 - - + -
104B ALA* 4.9 2.0 - - + -
105B VAL 3.0 12.2 + - - +
106B MET* 3.3 10.4 - - + +
107B VAL* 2.7 32.9 + - - +
156B ILE* 3.3 8.7 - - + +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 3.8 28.7 - - + -
83B ILE* 1.3 73.3 - - - +
85B GLY* 1.3 61.3 + - - +
107B VAL* 3.6 11.9 - - + -
141B ALA* 4.0 20.6 - - + -
145B LEU* 5.2 2.7 - - + -
155B VAL* 4.1 12.1 - - + -
156B ILE 2.9 7.4 + - - +
157B ILE* 4.1 10.5 - - + -
158B ASP* 2.7 30.0 + - - +
159B LEU* 3.8 29.6 - - + -
172B LEU* 4.3 4.7 - - + -
177B PHE* 4.9 9.2 - - + -
315B MTA 4.5 0.4 - - + -
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Residues in contact with GLY 85 (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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83B ILE* 3.6 13.9 - - - +
84B VAL* 1.3 80.3 - - - +
86B GLY* 1.3 61.5 + - - -
106B MET* 3.8 12.3 - - - +
107B VAL 3.0 12.5 + - - -
108B ASP* 3.4 20.1 - - - +
158B ASP* 3.6 6.1 - - - -
159B LEU* 4.6 0.7 - - - -
315B MTA 3.6 16.1 + - - -
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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