Contacts of the strand formed by residues 165 - 170 (chain A) in PDB entry 4BL5
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 PHE 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.5 33.4 - - + -
101A ALA* 4.2 1.1 - - + -
102A PHE* 3.9 26.9 - - + -
106A ALA 4.2 15.7 - - - -
107A ARG 5.3 0.4 - - - -
108A LYS* 4.7 1.8 - - - -
109A VAL* 3.4 34.1 - - + +
154A ASN* 3.3 37.1 - - - +
157A TYR* 3.9 32.3 - + + -
163A CYS* 3.1 27.9 + - + +
164A THR* 1.3 81.8 - - - +
166A THR* 1.3 61.6 + - - +
237A VAL* 3.4 15.5 - - - +
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Residues in contact with THR 166 (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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108A LYS* 4.5 12.8 - - - -
109A VAL 2.8 15.8 + - - +
110A VAL* 3.9 21.8 - - + -
111A SER* 3.0 18.9 + - - -
154A ASN* 3.0 15.9 + - - +
164A THR* 4.9 4.0 - - + +
165A PHE* 1.3 74.3 - - - +
167A ALA* 1.3 69.6 + - - +
230A VAL* 5.2 0.2 - - + -
234A TYR* 3.9 12.4 - - + -
236A GLU 3.0 24.0 + - - +
237A VAL* 2.6 23.0 + - - -
238A GLU 3.6 6.2 + - - -
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 4.1 2.9 - - - -
111A SER* 3.2 17.7 - - - +
113A LEU* 3.6 30.7 - - + -
151A ASP* 6.1 0.2 - - - -
154A ASN* 3.7 9.4 - - - +
166A THR* 1.3 87.5 + - - +
168A VAL* 1.3 66.0 + - - +
234A TYR* 4.9 0.5 - - - -
237A VAL 4.2 1.6 + - - -
239A PRO* 3.1 33.6 - - + +
240A ILE* 3.2 5.2 + - - +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 3.8 16.2 - - + -
111A SER 2.8 10.2 + - - +
112A CYS* 4.2 3.4 - - - -
113A LEU* 2.6 34.8 + - - +
167A ALA* 1.3 78.1 - - - +
169A ILE* 1.3 56.9 + - - +
170A PRO* 3.6 10.6 - - + +
227A PHE* 3.4 40.8 - - + -
230A VAL* 3.8 24.5 - - + -
240A ILE* 3.5 17.3 - - + +
242A LEU* 3.9 13.5 - - + -
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Residues in contact with ILE 169 (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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113A LEU* 4.0 10.5 - - + -
114A SER 3.5 32.3 - - - +
115A THR* 3.8 6.5 - - + +
117A ILE* 5.6 0.2 - - + -
118A PHE* 3.9 25.4 - - + -
128A GLU* 4.3 13.0 - - + -
131A ILE* 4.4 9.4 - - + -
168A VAL* 1.3 77.6 - - - +
170A PRO* 1.3 62.2 - - - +
171A THR 3.8 0.3 + - - -
239A PRO* 4.0 29.2 - - + -
240A ILE 3.0 11.2 + - - +
241A ILE* 3.5 26.3 - - + +
242A LEU* 3.1 18.3 + - - +
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Residues in contact with PRO 170 (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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19A VAL* 6.4 0.2 - - + -
112A CYS* 3.9 19.7 - - - -
113A LEU 3.0 26.2 - - - +
114A SER* 3.4 6.1 + - - -
115A THR* 3.1 22.5 + - - -
168A VAL* 3.6 9.6 - - + +
169A ILE* 1.3 83.7 - - - +
171A THR* 1.3 68.3 + - - +
173A VAL* 3.9 15.0 - - + -
218A ILE* 4.7 0.9 - - + -
223A LEU* 4.1 25.8 - - + -
227A PHE* 5.2 0.2 - - + -
242A LEU* 3.3 13.0 - - + +
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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