Contacts of the strand formed by residues 184 - 188 (chain A) in PDB entry 3U4S
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 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLN* 2.8 29.5 + - - -
75A VAL* 5.2 2.6 - - - +
84A GLN* 3.6 22.3 + - - -
121A TYR* 2.6 30.7 + - - -
125A LEU* 5.2 1.7 - - - +
132A TYR* 4.0 9.5 - - - -
182A LYS 3.3 13.7 + - - -
183A THR* 1.3 72.5 - - - +
185A PHE* 1.3 66.1 + - - +
186A ALA 4.2 0.4 - - - -
244A LEU* 4.2 10.8 - - - +
278A GLY 3.4 6.7 - - - -
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Residues in contact with PHE 185 (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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84A GLN* 5.2 0.4 - - - +
132A TYR* 5.0 1.6 - + + -
184A SER* 1.3 76.1 - - - +
186A ALA* 1.3 66.3 + - - +
188A HIS* 4.0 6.3 - + + -
206A LYS* 3.9 21.3 - - + -
207A SER 4.0 1.8 - - - -
208A TRP* 3.8 40.8 - + - -
244A LEU* 5.3 1.0 - - - +
276A HIS* 4.1 2.7 - + - -
277A ALA* 3.1 28.7 - - - +
278A GLY* 3.0 65.3 + - - +
279A PHE* 3.7 5.6 - - - -
280A ASN* 5.5 1.8 - - - -
503A 08P 3.2 53.2 - - + +
11C CYS* 5.7 1.1 - - + -
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Residues in contact with ALA 186 (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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84A GLN* 4.9 3.9 - - - +
184A SER 4.2 0.6 - - - -
185A PHE* 1.3 77.2 - - - +
187A TRP* 1.3 60.1 + - - +
188A HIS* 2.8 25.4 + - - +
241A LYS* 3.4 33.7 + - - +
243A THR 3.1 22.2 - - - +
244A LEU* 3.4 23.3 - - + +
276A HIS 3.3 2.9 - - - +
277A ALA* 3.7 3.1 - - - -
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Residues in contact with TRP 187 (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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122A TRP* 5.5 0.8 - - - -
186A ALA* 1.3 71.1 - - - +
188A HIS* 1.3 61.4 + - - +
209A TYR* 3.5 37.2 - + + -
210A SER 4.0 2.9 - - - -
211A VAL* 3.9 21.3 - - + -
219A LEU* 4.2 17.7 - - + -
238A LEU* 3.5 32.2 - - + +
241A LYS* 4.7 0.5 - - - -
243A THR* 2.9 17.6 + - - +
244A LEU* 4.3 0.9 - - - -
245A ILE* 3.0 56.2 + - + +
246A SER 6.1 0.2 - - - -
247A PRO* 6.2 0.4 - - + -
250A LEU* 3.7 23.1 - - + -
257A PHE* 5.1 0.2 - - + -
275A TYR* 3.5 32.1 - - + -
276A HIS* 3.3 31.6 - - - -
277A ALA* 3.5 12.2 - - + +
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Residues in contact with HIS 188 (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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185A PHE* 4.0 8.5 - + + -
186A ALA 2.8 23.1 + - - -
187A TRP* 1.3 74.6 - - - +
189A THR* 1.3 77.9 + - - +
190A GLU* 3.6 4.3 - - - -
238A LEU 4.3 7.6 - - - +
239A ARG* 5.3 2.0 - - - +
241A LYS* 3.7 36.9 - - + +
275A TYR* 3.4 16.1 - - - -
276A HIS* 2.9 44.7 + + - -
501A NI 2.2 43.1 - - + +
503A 08P 3.1 17.4 - - - -
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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