Contacts of the strand formed by residues 172 - 175 (chain B) in PDB entry 4AE6
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 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLU* 3.4 7.1 - - - +
128B MET* 2.9 54.6 + - + +
150B ILE* 4.1 9.0 - - + -
167B LEU* 4.0 18.6 - - + -
168B LYS 3.7 13.5 - - - +
169B PRO 3.2 7.5 + - - +
170B GLU 3.3 2.0 + - - -
171B ASN* 1.3 87.8 - - + +
173B LEU* 1.3 60.4 + - - +
180B ILE* 4.0 14.4 - - + -
181B GLN 3.5 2.2 - - - +
182B VAL* 3.8 27.4 - - + -
227B LEU* 3.8 30.5 - - + -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B VAL* 3.8 35.2 - - + +
125B GLY* 3.9 31.4 - - - +
126B GLY* 3.7 4.7 - - - +
127B GLU* 3.4 27.1 - - + +
172B LEU* 1.3 74.0 - - - +
174B ILE* 1.3 63.2 + - - +
175B ASP* 3.9 3.4 - - + -
180B ILE* 3.5 7.1 - - - +
181B GLN* 2.9 46.8 + - + +
183B THR* 3.8 19.8 - - + +
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Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLY* 3.2 2.7 - - - -
126B GLY 2.6 44.6 + - - +
128B MET* 4.2 22.7 - - + -
131B HIS* 3.9 27.8 - - + -
146B TYR* 3.3 37.5 - - + +
173B LEU* 1.3 74.5 - - - +
175B ASP* 1.3 63.8 + - - +
178B GLY* 3.8 26.5 - - - -
179B TYR 3.6 2.9 - - - -
180B ILE* 4.3 10.3 - - + -
314B PHE* 4.3 7.4 - - + -
316B PRO* 3.4 17.8 - - + +
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Residues in contact with ASP 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B VAL* 3.3 31.6 - - + +
124B PRO 3.8 6.3 - - - -
125B GLY* 4.0 1.3 - - - -
173B LEU* 3.9 5.4 - - + -
174B ILE* 1.3 77.2 - - - +
176B GLN* 1.3 58.9 + - - +
177B GLN* 2.9 17.7 + - - +
178B GLY 2.8 21.3 + - - -
179B TYR* 2.9 35.0 + - - +
180B ILE 4.7 2.9 - - - +
181B GLN* 4.8 7.8 - - + +
308B ARG* 2.9 28.8 + - - -
316B PRO* 3.3 11.5 - - - +
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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