Contacts of the strand formed by residues 163 - 167 (chain A) in PDB entry 5LXX
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 SER 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A HIS* 2.6 33.9 + - - -
139A VAL 3.1 20.9 + - - -
161A VAL* 3.5 11.1 - - - +
162A ASN* 1.3 81.2 - - - +
164A PHE* 1.3 63.5 + - - +
193A ALA* 4.1 1.0 - - - +
194A ILE* 3.4 13.2 - - - +
196A GLN* 4.6 4.7 - - - -
392A PHE* 3.8 17.5 - - - -
471A ARG* 2.9 17.7 + - - +
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Residues in contact with PHE 164 (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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116A LEU* 4.6 0.4 - - + -
139A VAL* 3.1 37.9 - - + +
141A ILE* 3.9 18.2 - - + -
152A MET* 3.5 56.1 - - + -
155A LEU* 4.2 10.3 - - + -
156A VAL* 3.6 23.3 - - + -
161A VAL* 3.9 15.7 - - + -
163A SER* 1.3 74.3 - - - +
165A LEU* 1.3 55.6 + - - +
166A VAL* 5.7 0.2 - - - +
188A ILE* 4.0 12.1 - - + +
191A ILE* 4.0 7.2 - - + -
193A ALA* 3.9 18.4 - - + -
194A ILE 3.1 6.2 + - - +
195A ALA* 3.7 2.3 - - - -
196A GLN* 2.7 35.2 + - - +
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Residues in contact with LEU 165 (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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75A ARG* 4.1 8.3 - - - +
107A HIS* 3.8 15.7 - - + -
139A VAL 3.0 6.7 + - - +
140A ASP* 3.5 18.4 - - - +
141A ILE* 2.8 33.8 + - - +
164A PHE* 1.3 75.1 - - - +
166A VAL* 1.3 71.2 + - - +
167A TYR* 3.2 41.5 - - + +
196A GLN* 3.3 17.5 - - + +
197A VAL 4.3 2.9 - - - -
198A HIS* 4.2 4.5 - - + +
253A THR* 3.6 36.6 - - + +
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Residues in contact with VAL 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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141A ILE* 4.2 11.7 - - + -
165A LEU* 1.3 83.3 - - - +
167A TYR* 1.3 59.8 + - - +
176A LEU* 3.8 23.3 - - + -
181A ILE* 4.4 19.7 - - + -
184A VAL* 3.7 30.5 - - + -
185A LEU* 4.4 13.7 - - + -
188A ILE* 5.3 2.7 - - + -
196A GLN 2.9 15.8 + - - +
197A VAL* 3.3 21.7 - - + +
198A HIS 2.9 24.4 + - - -
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Residues in contact with TYR 167 (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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75A ARG* 3.7 24.7 + - - -
109A VAL* 5.6 1.4 - - + +
140A ASP* 3.7 11.9 + - + -
141A ILE 4.2 11.1 + - - -
165A LEU* 3.2 24.0 - - + -
166A VAL* 1.3 75.4 - - - +
168A MET* 1.3 62.1 + - - +
169A ALA 3.4 13.0 - - - +
170A PHE* 3.2 39.3 - + - -
174A PHE* 3.6 45.3 + + + +
176A LEU* 2.9 33.8 + - - +
181A ILE* 4.5 1.0 - - - +
198A HIS* 3.3 28.6 + + + -
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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