Contacts of the strand formed by residues 152 - 158 (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 TYR 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B ARG* 3.4 30.3 - - + +
81B VAL 3.9 9.9 - - - -
82B LEU* 3.9 33.2 - - + +
105B VAL* 3.7 16.6 - - + +
144B TYR* 2.9 35.1 + + - -
150B GLU* 3.4 40.3 + - + +
151B ARG* 1.3 81.5 - - - +
153B ASP* 1.3 56.6 + - - +
154B VAL 4.0 10.5 - - - +
155B VAL* 4.8 1.6 - - + -
184B HIS* 2.8 32.5 + + + +
185B LEU* 3.2 12.3 - - + +
186B ASN* 2.5 40.2 + - - +
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Residues in contact with ASP 153 (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 HIS* 3.6 34.3 + - + +
77B GLU 4.4 0.5 - - - +
78B PRO* 4.0 9.1 - - + +
79B LYS* 3.0 32.0 + - - +
80B ARG* 2.9 19.3 + - - +
152B TYR* 1.3 72.6 - - - +
154B VAL* 1.3 59.6 + - - +
185B LEU* 3.8 2.2 - - - +
186B ASN* 2.7 32.1 + - - +
189B GLY* 2.9 10.0 - - - -
190B VAL 2.9 26.2 + - - +
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Residues in contact with VAL 154 (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 ALA* 3.9 20.4 - - + +
72B MET* 3.9 23.3 - - - -
75B HIS* 4.3 5.2 - - + -
78B PRO* 4.2 16.8 - - + -
80B ARG 3.4 4.0 + - - +
81B VAL* 3.2 15.9 - - + +
82B LEU 2.8 23.0 + - - -
152B TYR* 4.0 2.7 - - - +
153B ASP* 1.3 81.5 - - - +
155B VAL* 1.3 79.4 + - - +
156B ILE* 3.6 21.3 - - + -
190B VAL* 3.3 13.5 - - + +
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Residues in contact with VAL 155 (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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82B LEU* 3.3 35.2 - - + +
84B VAL* 4.1 4.5 - - + -
152B TYR* 4.8 4.7 - - + -
153B ASP 4.3 0.2 - - - -
154B VAL* 1.3 87.4 - - - +
156B ILE* 1.3 71.0 + - - +
157B ILE* 3.8 16.4 - - + -
181B VAL* 3.4 37.0 - - + +
184B HIS* 5.3 0.9 - - + +
185B LEU* 3.8 22.4 - - + -
190B VAL 3.2 6.0 + - - +
191B MET* 4.5 9.4 - - + -
192B GLY 3.1 23.7 + - - -
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Residues in contact with ILE 156 (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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67B LEU* 3.9 41.7 - - + +
68B VAL* 4.2 12.8 - - + +
71B ALA* 3.7 20.4 - - + -
72B MET* 5.4 0.9 - - + -
81B VAL* 4.6 6.5 - - + -
82B LEU 2.7 14.1 + - - +
83B ILE* 3.3 6.8 - - + +
84B VAL 2.9 27.0 + - - +
91B THR* 4.1 14.6 - - + -
95B VAL* 4.9 5.8 - - + -
154B VAL* 3.6 18.8 - - + -
155B VAL* 1.3 85.2 - - - +
157B ILE* 1.3 65.0 + - - +
192B GLY 3.1 17.0 - - - +
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Residues in contact with ILE 157 (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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67B LEU* 4.4 0.2 - - - +
84B VAL* 3.7 12.3 - - + -
155B VAL* 3.8 16.8 - - + -
156B ILE* 1.3 75.5 - - - +
158B ASP* 1.3 58.0 + - - +
159B LEU* 3.3 33.1 + - + -
172B LEU 5.6 0.2 - - - +
173B TYR* 5.7 0.4 - - - +
177B PHE* 4.3 21.5 - - + -
178B TYR* 4.7 0.9 - - + -
181B VAL* 4.3 4.3 - - + -
191B MET* 3.0 39.3 - - + -
192B GLY 3.2 4.2 + - - -
193B MET* 3.5 27.9 - - + -
194B GLN* 3.3 24.8 + - - +
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Residues in contact with ASP 158 (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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63B TYR* 2.8 28.0 + - - -
67B LEU* 3.7 19.5 - - + -
84B VAL 2.7 17.0 + - - +
85B GLY* 3.6 0.7 - - - -
86B GLY* 3.2 32.7 + - - +
88B GLU* 4.0 7.1 - - - +
91B THR* 2.6 35.5 + - + +
156B ILE* 3.7 1.5 + - + -
157B ILE* 1.3 72.0 - - - +
159B LEU* 1.3 65.7 + - - +
194B GLN* 4.9 1.5 - - - +
315B MTA 3.7 8.6 - - - +
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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