Contacts of the strand formed by residues 140 - 144 (chain A) in PDB entry 4B0O
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 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL* 3.9 20.2 - - + -
98A TRP 3.4 10.1 - - - +
99A ILE* 3.8 13.9 - - + -
100A PRO* 4.0 9.4 - - + -
104A PRO* 4.2 3.1 - - + -
107A ALA* 4.2 7.1 - - + +
108A THR 3.0 10.6 + - - +
109A VAL* 3.4 7.5 - - + -
110A LEU* 2.8 28.1 + - - +
139A VAL* 1.3 75.7 - - - +
141A VAL* 1.3 62.7 + - - +
142A VAL* 4.1 7.6 - - + -
182A ILE* 4.1 15.7 - - + -
185A PHE 3.7 16.6 - - - +
186A GLY 3.8 4.0 - - - +
187A GLY* 3.4 38.1 - - - +
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A VAL* 3.4 2.6 - - - -
98A TRP* 2.9 54.2 + - + +
110A LEU* 3.4 13.0 - - + +
112A TRP* 5.3 2.0 - - + -
128A TYR 5.5 0.2 - - - +
130A GLY* 3.6 39.0 - - - +
133A LEU* 3.7 25.6 - - + -
134A ALA* 4.4 2.7 - - - +
139A VAL* 4.3 9.0 - - + +
140A ILE* 1.3 76.6 - - - +
142A VAL* 1.3 69.8 + - - +
143A SER* 5.6 0.4 - - - -
195A PHE* 4.9 6.7 - - + -
446A PHE* 4.6 12.8 - - + -
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.6 12.8 - - + -
96A ASN 3.2 9.6 - - - +
97A VAL* 4.2 12.8 - - + -
98A TRP* 5.1 0.2 - - - -
109A VAL* 3.8 20.4 - - + -
110A LEU 2.8 7.1 + - - +
111A ILE* 3.2 19.9 - - + +
112A TRP* 2.7 32.6 + - - +
140A ILE* 4.1 3.1 - - + -
141A VAL* 1.3 80.6 - - - +
143A SER* 1.3 64.8 + - - +
144A MET* 5.8 1.8 - - + -
174A ALA* 6.2 1.6 - - + -
178A VAL* 3.9 20.0 - - + -
182A ILE* 4.1 21.1 - - + -
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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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95A LEU* 3.2 4.0 - - - +
96A ASN* 2.7 63.8 + - - -
98A TRP* 3.7 16.5 - - - -
111A ILE* 5.2 0.4 - - - -
112A TRP* 3.7 27.1 - - - -
123A SER* 3.5 15.5 + - - -
128A TYR 5.5 2.9 - - - -
141A VAL* 5.6 0.7 - - - -
142A VAL* 1.3 77.6 - - - +
144A MET* 1.3 61.4 + - - +
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Residues in contact with MET 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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33A TYR* 3.9 6.1 - - + +
94A TYR 3.5 6.1 - - - +
95A LEU* 3.8 14.8 - - + +
111A ILE* 3.8 29.4 - - + -
112A TRP 3.9 10.1 + - - +
113A ILE* 4.1 16.6 - - + -
114A TYR* 3.3 19.6 - - - -
123A SER* 3.9 3.3 - - - -
142A VAL* 5.8 1.3 - - + -
143A SER* 1.3 76.4 - - - +
145A ASN* 1.3 75.3 - - - +
146A TYR* 3.9 5.5 + - + +
171A GLN* 4.2 25.4 - - - +
174A ALA* 3.8 31.4 - - + -
175A LEU* 4.2 9.4 - - + -
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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