Contacts of the strand formed by residues 152 - 158 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ARG* 3.5 9.9 - - + +
81A VAL 3.6 22.7 - - - -
82A LEU* 3.7 36.1 - - + -
103A LYS* 6.0 0.4 - - + -
105A VAL* 3.7 28.4 - - + +
144A TYR* 2.8 33.1 + + - -
148A THR* 5.9 0.2 - - + -
150A GLU* 3.9 29.4 + - + +
151A ARG* 1.4 82.1 - - - +
153A ASP* 1.3 62.4 + - - +
154A VAL 3.7 15.0 - - - +
155A VAL* 4.4 2.7 - - + -
184A HIS* 3.3 23.5 + + + +
185A LEU* 3.3 14.3 - - + +
186A ASN* 2.9 29.5 + - - +
189A GLY* 4.7 0.3 - - - -
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Residues in contact with ASP 153 (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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75A HIS* 3.4 30.1 + - + +
77A GLU 4.5 1.7 - - - +
78A PRO* 4.1 2.9 - - + -
79A LYS* 2.9 37.2 + - - +
80A ARG* 2.6 27.2 + - - +
152A TYR* 1.3 74.8 - - - +
154A VAL* 1.3 61.5 + - - +
185A LEU* 4.2 1.1 - - - -
186A ASN* 3.4 24.1 - - - +
187A PRO 5.0 2.3 - - - +
189A GLY* 2.9 28.3 - - - -
190A VAL 2.9 5.8 + - - -
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Residues in contact with VAL 154 (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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71A ALA* 3.7 19.5 - - + +
72A MET* 4.1 20.9 - - - -
75A HIS* 4.1 14.6 - - + -
78A PRO* 4.8 2.9 - - + -
80A ARG 3.5 3.0 + - - -
81A VAL* 3.3 11.1 - - + +
82A LEU 3.0 22.0 + - - -
152A TYR* 3.7 5.4 - - - +
153A ASP* 1.3 83.5 - - - +
155A VAL* 1.3 63.4 + - - +
156A ILE* 3.4 32.5 - - + -
190A VAL* 3.2 32.1 - - + +
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Residues in contact with VAL 155 (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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82A LEU* 3.2 32.5 - - + +
84A VAL* 4.2 8.7 - - + -
145A LEU* 6.3 0.4 - - + -
152A TYR* 4.4 10.1 - - + -
154A VAL* 1.3 75.7 - - - +
156A ILE* 1.3 72.4 + - - +
157A ILE* 4.2 5.4 - - + -
181A VAL* 3.8 34.1 - - + +
184A HIS* 5.1 1.3 - - + +
185A LEU* 3.3 27.8 - - + -
190A VAL 3.2 4.2 + - - -
191A MET* 3.4 5.2 - - + +
192A GLY 2.8 25.3 + - - +
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Residues in contact with ILE 156 (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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67A LEU* 3.8 43.1 - - + +
68A VAL* 4.0 11.2 - - + +
71A ALA* 3.6 19.3 - - + -
72A MET* 5.1 2.2 - - + -
81A VAL* 4.9 2.7 - - + -
82A LEU 2.7 12.4 + - - +
83A ILE* 3.4 4.2 - - + +
84A VAL* 2.7 33.8 + - - +
91A THR* 3.9 16.8 - - + -
95A VAL* 4.5 20.4 - - + -
154A VAL* 3.4 26.9 - - + -
155A VAL* 1.3 76.7 - - - +
157A ILE* 1.3 59.0 + - - +
158A ASP* 4.1 2.0 - - + +
192A GLY* 3.4 5.2 - - - +
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Residues in contact with ILE 157 (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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67A LEU* 3.9 1.4 - - - +
84A VAL* 3.7 13.2 - - + -
155A VAL* 4.2 9.6 - - + -
156A ILE* 1.3 75.4 - - - +
158A ASP* 1.4 63.2 + - - +
159A LEU* 3.6 27.8 + - + +
172A LEU 6.0 0.2 - - - +
173A TYR* 5.8 1.1 - - + +
177A PHE* 3.4 35.0 - - + -
178A TYR* 4.9 7.4 - - + -
181A VAL* 3.8 12.1 - - + -
191A MET* 4.3 13.0 - - - -
192A GLY 2.8 11.1 + - - +
193A MET* 3.1 24.5 - - + +
194A GLN 3.1 28.0 + - - +
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Residues in contact with ASP 158 (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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54A GLN* 5.7 0.3 - - - +
63A TYR* 2.3 37.8 + - - -
64A HIS* 4.9 2.9 + - - -
67A LEU* 3.5 22.0 - - + +
83A ILE* 5.4 1.3 - - + -
84A VAL 2.9 13.8 + - - +
85A GLY* 3.4 3.5 - - - -
86A GLY* 3.0 44.9 + - - +
88A GLU* 4.8 5.0 - - - +
91A THR* 3.4 12.5 + - + +
156A ILE* 4.1 4.2 - - + -
157A ILE* 1.4 73.6 - - - +
159A LEU* 1.3 59.7 + - - +
194A GLN* 4.0 3.1 - - - +
315A MTA 3.2 15.0 - - - +
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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