Contacts of the strand formed by residues 176 - 180 (chain L) in PDB entry 5A0Q
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 LEU 176 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L ILE* 3.9 20.6 - - + -
14L VAL 3.5 4.5 - - - -
15L ALA* 3.9 7.2 - - + +
153L TYR* 3.7 44.2 - - + +
156L ALA* 4.1 4.5 - - + -
157L ARG* 3.7 20.2 - - + +
174L VAL* 3.5 28.7 - - + -
175L ASN* 1.3 73.7 - - - +
177L TYR* 1.3 61.3 + - - +
186L ARG* 2.9 20.8 + - - -
187L VAL* 3.3 27.4 + - + -
188L SER* 3.0 20.0 + - - +
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Residues in contact with TYR 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L VAL 4.7 0.2 - - - -
13L ILE* 3.4 6.2 - - - +
14L VAL* 2.9 42.9 + - + +
32L LYS* 3.8 22.1 - - + +
34L VAL* 3.3 45.1 + - + +
36L GLU* 6.4 0.4 - - + -
42L LEU* 3.6 17.5 - - + -
175L ASN* 3.3 20.6 - - + -
176L LEU* 1.3 73.9 - - - +
178L HIS* 1.3 61.1 + - - +
179L VAL* 4.0 2.0 - - + -
184L TRP* 3.5 39.9 - + + -
185L ILE 3.3 7.4 - - - +
186L ARG* 3.3 36.4 + - - -
187L VAL* 4.1 1.3 - - - +
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Residues in contact with HIS 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L PHE* 4.2 2.3 - + - -
10L HIS 2.9 28.1 + - - -
11L GLY* 3.1 10.1 - - - -
12L VAL 3.6 9.4 - - - -
13L ILE* 4.0 12.8 - - + -
149L VAL* 3.5 23.3 - - + -
153L TYR* 2.7 22.6 + + + +
177L TYR* 1.3 74.5 - - - +
179L VAL* 1.3 66.2 + - - +
180L ARG* 3.4 28.4 + - + +
183L GLY 3.4 4.5 - - - +
184L TRP* 2.9 19.8 - - - -
185L ILE* 3.1 14.4 + - + +
187L VAL* 3.0 23.0 - - + +
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Residues in contact with VAL 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L GLY* 3.5 1.0 - - - -
12L VAL* 2.7 38.6 + - + +
14L VAL* 4.6 8.1 - - + -
40L TYR 3.5 24.2 - - - +
42L LEU* 5.4 8.3 - - + +
102L CYS* 4.5 15.3 - - + +
103L GLY* 3.8 21.3 - - - -
104L TRP* 3.8 6.2 - - + +
177L TYR* 5.1 2.5 - - + -
178L HIS* 1.3 77.9 - - - +
180L ARG* 1.3 69.9 + - - +
183L GLY* 3.9 3.1 - - - -
184L TRP* 3.8 26.7 - - + +
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Residues in contact with ARG 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L HIS 4.0 5.4 - - - +
11L GLY* 4.0 5.4 - - - -
104L TRP* 3.4 14.8 - - - +
178L HIS* 3.4 34.3 - - + +
179L VAL* 1.3 79.1 - - - +
181L GLU* 1.3 69.2 + - + +
182L ASP* 4.1 22.3 + - - +
183L GLY 3.2 28.7 + - - +
185L ILE* 3.4 43.6 - - - +
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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