Contacts of the strand formed by residues 142 - 145 (chain A) in PDB entry 4UC5
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 ALA 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A VAL* 3.9 2.2 - - - -
93A MET 3.7 5.2 - - - -
95A VAL* 3.7 11.2 - - + -
132A LEU* 3.5 32.3 - - + -
135A LEU* 4.5 7.4 - - + -
136A ASN* 4.5 6.9 + - - +
140A MET 4.7 0.9 - - - +
141A PRO* 1.3 76.3 - - - +
143A SER* 1.3 61.8 + - - +
158A LEU 4.2 10.5 + - - +
159A ILE* 3.8 2.3 - - + -
160A SER* 2.9 33.8 + - - +
161A TRP 3.6 0.5 + - - -
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Residues in contact with SER 143 (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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59A ILE* 3.5 19.6 - - - +
92A VAL* 3.7 13.0 - - - -
93A MET 2.8 19.4 + - - -
94A ARG* 3.5 4.9 - - - +
95A VAL* 2.7 28.1 + - - +
96A TYR* 4.4 1.8 - - - -
142A ALA* 1.3 75.2 - - - +
144A THR* 1.3 64.0 + - - +
159A ILE* 4.4 2.7 - - - -
161A TRP* 3.1 33.6 - - - -
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Residues in contact with THR 144 (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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95A VAL 2.6 26.1 + - - -
96A TYR* 3.7 17.0 - - - -
97A PHE* 3.9 12.3 + - - -
143A SER* 1.3 71.6 - - - +
145A GLU* 1.3 70.6 + - - +
146A PHE* 3.9 28.3 + - + -
155A TYR* 4.2 9.1 + - + -
159A ILE* 3.6 24.0 - - + -
161A TRP* 3.2 6.1 + - - +
162A GLY* 3.3 6.8 - - - -
163A ALA* 2.9 23.2 + - - +
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Residues in contact with GLU 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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96A TYR* 3.6 36.1 - - + +
97A PHE* 5.9 0.9 + - - -
98A GLU 4.7 3.2 - - - +
100A PRO* 4.2 17.3 - - - +
144A THR* 1.3 84.7 + - - +
146A PHE* 1.3 67.1 + - - +
147A LEU* 3.4 36.5 + - + +
155A TYR* 5.0 4.3 + - - -
163A ALA* 3.2 21.8 - - + +
165A GLY* 3.2 29.3 + - - -
168A THR* 4.1 5.0 + - - -
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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