Contacts of the strand formed by residues 144 - 147 (chain A) in PDB entry 4WNO
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 ILE 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP* 3.4 2.4 - - - -
100A LEU* 2.8 61.0 + - + +
118A PHE* 6.4 0.2 - - + -
122A ILE* 4.3 18.2 - - + -
139A LEU* 4.9 6.7 - - + -
140A LYS 3.6 13.7 - - - +
141A PRO* 3.2 3.1 + - + +
142A GLN 3.4 0.2 - - - -
143A ASN* 1.3 83.9 - - + +
145A LEU* 1.3 61.4 + - - +
161A VAL* 3.8 31.0 - - + -
162A LYS 3.6 3.4 - - - +
163A ILE* 3.9 30.1 - - + -
210A ILE* 4.2 17.7 - - + -
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Residues in contact with LEU 145 (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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76A VAL* 4.1 5.6 - - + -
95A CYS* 3.8 17.0 - - + -
98A GLY 3.5 4.3 - - - +
99A ASP* 3.7 20.4 - - + -
142A GLN 4.0 11.2 - - - +
143A ASN 4.6 0.9 - - - -
144A ILE* 1.3 82.0 - - - +
146A LEU* 1.3 63.4 + - - +
161A VAL* 3.2 5.9 - - - +
162A LYS* 2.7 41.9 + - - +
164A ALA* 3.9 16.6 - - + -
401A 3RF 3.5 70.4 - - + +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A CYS* 3.3 10.9 - - - +
97A GLY* 2.8 42.9 + - - +
98A GLY 2.8 6.9 + - - -
99A ASP 3.8 2.2 - - - -
100A LEU* 3.7 38.8 - - + +
103A TYR* 3.6 39.5 - - + -
118A PHE* 4.7 0.4 - - + -
144A ILE 4.2 0.2 - - - +
145A LEU* 1.3 78.1 - - - +
147A SER* 1.3 63.6 + - - +
159A ILE* 3.6 30.3 - - + -
160A ARG 3.5 3.8 - - - -
161A VAL* 4.2 11.2 - - + -
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Residues in contact with SER 147 (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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93A GLU* 5.2 1.2 + - - -
94A TYR 4.1 4.3 + - - -
95A CYS* 3.8 10.0 - - - -
96A ASN* 3.3 28.1 + - - -
97A GLY* 4.1 0.9 - - - +
146A LEU* 1.3 78.8 - - - +
148A ASN* 1.3 62.9 + - - +
149A PRO* 4.0 0.8 - - - +
159A ILE* 4.7 2.0 - - - -
160A ARG* 2.8 38.9 + - - +
162A LYS* 4.0 23.8 - - - -
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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