Contacts of the strand formed by residues 180 - 184 (chain B) in PDB entry 5I2Y
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 ARG 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLN* 3.5 1.6 - - - -
117B LEU* 2.9 28.7 + - + +
177B THR* 3.2 35.1 + - - +
178B GLU 4.7 2.0 - - - +
179B GLY* 1.3 79.9 - - - +
181B LEU* 1.3 67.8 + - - +
182B LEU* 4.6 0.2 - - - +
211B LEU* 3.5 32.7 - - + +
212B LEU 2.8 28.0 + - - -
213B PRO* 3.7 24.9 - - - +
214B THR 3.4 5.8 - - - -
215B GLU* 4.0 21.5 - - + +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 4.5 4.5 - - + -
94A VAL 4.1 5.4 - - - +
95A LEU* 3.4 32.8 - - + -
95B LEU* 3.8 22.2 - - + -
114B ALA* 5.3 0.9 - - + -
115B GLY 3.3 23.3 - - - +
116B GLN* 3.8 13.0 - - + +
179B GLY 5.5 0.4 - - - +
180B ARG* 1.3 80.3 - - - +
182B LEU* 1.3 62.0 + - - +
211B LEU* 4.3 3.1 - - - +
212B LEU* 3.3 47.7 + - + +
214B THR* 3.0 34.1 + - + +
216B GLN* 4.8 8.7 - - - +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ARG 3.5 2.3 - - - +
114B ALA* 3.4 3.4 - - - -
115B GLY* 2.7 36.3 + - - +
116B GLN 5.1 0.2 - - - -
117B LEU* 4.6 14.6 - - + +
144B LEU* 3.6 30.5 - - + -
146B VAL* 4.2 15.3 - - + -
157B VAL* 5.9 0.4 - - + -
174B PHE* 4.1 10.1 - - + -
177B THR* 5.8 0.9 - - - +
180B ARG 4.6 3.1 - - - +
181B LEU* 1.3 77.2 - - - +
183B LEU* 1.3 59.6 + - - +
184B LEU* 3.8 24.4 + - + +
209B PHE* 4.3 7.0 - - + -
210B SER 3.9 7.2 - - - +
211B LEU* 3.5 34.8 - - + -
212B LEU* 4.4 2.0 - - - +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 3.5 27.4 - - + -
185A GLN* 4.0 7.6 - - - +
210A SER* 5.5 0.2 - - - +
212A LEU* 3.9 19.1 - - + -
112B PRO* 3.8 19.7 - - + -
113B ARG 3.7 17.5 - - - +
114B ALA* 4.2 6.7 - - + +
182B LEU* 1.3 72.6 - - - +
184B LEU* 1.3 60.2 + - - +
185B GLN* 3.8 32.5 + - + +
209B PHE* 3.2 8.8 - - - +
210B SER* 2.7 48.3 + - - +
212B LEU* 4.1 13.8 - - + +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 4.0 28.0 - - + -
111B SER 4.5 0.3 - - - +
112B PRO* 3.2 2.1 - - - +
113B ARG* 2.7 41.2 + - + +
146B VAL* 4.7 7.2 - - + -
155B CYS* 4.0 24.7 - - + -
157B VAL* 5.9 2.0 - - + -
182B LEU* 3.9 31.9 - - + +
183B LEU* 1.3 80.3 - - - +
185B GLN* 1.3 61.1 + - - +
186B ASP 3.8 1.3 - - - -
187B CYS* 3.6 20.1 - - - -
204B LEU* 4.5 4.7 - - + -
206B VAL* 4.1 25.6 - - + -
208B ARG 3.8 3.4 - - - -
209B PHE* 4.4 3.6 - - + -
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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
------------------------------------------------------------
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