Contacts of the strand formed by residues 251 - 255 (chain B) in PDB entry 4A69
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 CYS 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 4.2 13.5 - - - -
157B LEU* 3.6 41.1 - - + -
161B HIS* 3.7 22.2 - - + +
163B ARG 3.5 1.8 + - - -
164B VAL* 3.5 8.4 - - + -
165B LEU 2.9 25.3 + - - -
249B PRO* 3.8 2.6 - - - +
250B THR* 1.3 81.0 + - - +
252B ILE* 1.3 73.1 + - - +
288B ILE* 3.9 0.7 - - - -
289B PRO* 3.6 19.5 - - - -
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 3.3 31.2 - - + +
167B ILE* 4.3 11.7 - - + -
240B ILE* 6.2 0.4 - - + -
244B VAL* 4.5 7.9 - - + -
249B PRO* 4.2 3.8 - - + -
251B CYS* 1.3 80.9 - - - +
253B VAL* 1.3 74.4 + - - +
254B LEU 4.3 0.7 - - - +
283B VAL* 3.8 28.3 - - + +
286B PHE* 4.8 4.3 - - + -
288B ILE* 3.9 32.5 - - + +
289B PRO 2.8 14.3 + - - +
290B LEU* 3.4 22.0 - - + +
291B LEU 2.8 25.5 + - - -
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ILE* 4.4 6.5 - - + -
154B ILE* 3.9 17.5 - - + -
157B LEU* 3.6 30.5 - - + -
164B VAL* 4.2 4.7 - - + -
165B LEU 2.8 11.0 + - - +
166B TYR* 3.3 24.4 - - + -
167B ILE* 2.8 31.9 + - - +
252B ILE* 1.3 77.1 - - - +
254B LEU* 1.3 57.2 + - - +
291B LEU* 3.5 20.0 - - + +
293B LEU* 3.9 27.6 - - + -
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Residues in contact with LEU 254 (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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167B ILE* 3.4 32.3 - - + +
169B ILE* 4.5 11.4 - - + -
236B PHE* 4.9 1.3 - - + -
252B ILE* 4.1 1.5 - - + -
253B VAL* 1.3 73.9 - - - +
255B GLN* 1.3 66.9 + - - +
256B CYS* 3.6 23.6 + - - -
279B CYS 5.0 0.9 - - - +
280B VAL* 3.9 31.4 - - + +
283B VAL* 4.1 25.8 - - + -
290B LEU* 4.2 14.4 - - + -
291B LEU 2.9 12.8 + - - +
292B VAL* 3.7 6.9 - - + -
293B LEU* 3.0 28.7 + - - +
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Residues in contact with GLN 255 (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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132B GLY* 2.8 37.0 + - - +
134B HIS* 3.8 11.7 + - - -
150B ILE* 3.7 4.8 - - + +
166B TYR* 3.5 20.7 - - + +
167B ILE 2.8 13.5 + - - +
168B ASP* 3.3 19.7 - - - +
169B ILE* 3.2 24.1 + - - +
170B ASP* 3.0 33.8 + - + +
253B VAL 4.1 1.0 + - - -
254B LEU* 1.3 73.7 - - - +
256B CYS* 1.3 58.7 + - - +
257B GLY 3.8 4.2 - - - +
293B LEU* 3.9 7.2 - - + -
294B GLY 3.1 14.1 + - - +
295B GLY* 3.6 7.7 - - - -
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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