Contacts of the strand formed by residues 154 - 158 (chain D) 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 VAL 154 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D PRO* 3.5 28.7 - - + +
71D ILE* 3.7 29.6 - - + -
93D GLU* 2.7 18.8 + - + +
94D VAL* 3.3 16.6 - - + +
95D ARG 3.1 24.6 + - - -
152D ALA* 3.5 4.7 - - - +
153D ARG* 1.3 107.7 - - - +
155D LEU* 1.3 58.4 + - - +
258D ILE* 4.1 14.6 - - + -
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D TYR* 4.9 5.4 - - + -
68D MET* 4.2 21.8 - - + +
69D PRO 3.7 4.7 + - - +
70D LEU* 3.2 28.1 - - + +
71D ILE* 3.0 21.1 + - - +
95D ARG* 3.4 48.7 - - + +
142D LEU* 5.3 2.5 - - + +
145D ILE* 3.7 13.0 - - + -
146D ALA* 3.6 28.0 - - + +
151D PRO* 5.3 0.4 - - + -
152D ALA 4.4 21.5 - - - +
153D ARG 4.1 1.8 + - - -
154D VAL* 1.3 74.8 - - - +
156D CYS* 1.3 59.4 + - - +
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Residues in contact with CYS 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LEU* 5.2 0.4 - - - -
71D ILE* 3.1 36.3 - - + +
73D VAL* 4.0 9.6 - - - -
94D VAL* 4.4 2.0 - - + -
95D ARG* 2.8 12.7 + - - +
96D CYS* 2.0 64.2 - - - +
145D ILE* 3.9 12.8 - - - +
148D HIS* 5.1 0.5 + - - -
155D LEU* 1.3 74.7 - - - +
157D ASN* 1.3 81.9 + - - +
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Residues in contact with ASN 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ILE 2.7 9.5 + - - -
72D PHE* 3.5 17.2 - - + -
73D VAL 3.0 25.3 + - - +
96D CYS 4.2 2.7 - - - -
98D GLU 4.4 4.4 + - - -
100D THR* 3.2 32.3 - - - +
103D ILE* 3.6 14.3 - - - +
145D ILE* 4.0 22.8 - - + +
148D HIS* 4.6 4.4 + - - -
156D CYS* 1.3 79.4 - - - +
158D LYS* 1.3 67.5 + - - +
159D ASP* 3.6 21.3 + - - +
162D THR* 4.2 9.2 - - - +
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Residues in contact with LYS 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D A3P 5.2 0.8 + - - -
73D VAL* 3.4 28.0 - - + +
81D THR* 3.4 30.5 + - - +
82D THR* 3.3 40.0 + - - +
85D ARG* 3.8 26.2 - - + +
96D CYS 4.6 4.4 + - - -
97D GLY 4.6 4.5 - - - +
98D GLU 3.7 2.2 + - - +
99D GLU* 2.8 63.9 + - - +
156D CYS* 4.5 0.4 - - - -
157D ASN* 1.3 76.3 - - - +
159D ASP* 1.3 61.8 + - - +
160D PRO* 3.9 8.3 - - + -
283D GLU* 4.7 2.4 + - - -
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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