Contacts of the strand formed by residues 186 - 194 (chain A) in PDB entry 5T4S
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 TYR 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A SER* 3.2 27.8 + - - -
182A ASP 3.3 31.2 - - - -
183A PRO* 3.0 37.3 + - + +
184A GLN 3.7 0.2 - - - -
185A HIS* 1.3 78.9 - - - +
187A GLU* 1.3 64.6 + - - +
188A GLY 4.2 12.6 - - - -
190A PHE* 3.4 27.5 - + - -
324A TYR* 3.6 31.4 - + + -
337A ALA* 3.9 11.7 - - + -
338A LEU 3.2 11.4 - - - +
340A ARG* 3.3 13.4 + - - +
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Residues in contact with GLU 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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186A TYR* 1.3 78.2 - - - +
188A GLY* 1.3 69.7 + - - +
189A ASN 4.6 0.3 - - - +
337A ALA* 3.9 3.5 - - - +
338A LEU* 2.9 50.7 + - + +
339A ALA 4.5 4.0 - - - +
340A ARG* 3.6 24.8 - - + +
7B THR 5.1 2.9 - - - +
8B SER* 3.6 3.3 - - - -
9B SER* 2.5 54.0 + - - +
100B GLY* 3.4 9.7 - - - -
101B GLY* 3.9 16.6 - - - +
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Residues in contact with GLY 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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186A TYR* 4.2 14.0 - - - -
187A GLU* 1.3 82.0 - - - +
189A ASN* 1.3 65.5 + - - -
190A PHE 4.1 0.5 + - - -
101B GLY* 3.6 26.7 + - - -
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Residues in contact with ASN 189 (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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187A GLU 4.6 0.7 - - - +
188A GLY* 1.3 77.3 + - - -
190A PHE* 1.3 71.1 + - - +
191A HIS* 3.4 28.7 + - + +
336A PHE 3.7 4.5 - - - +
337A ALA* 3.8 8.4 - - - +
338A LEU 5.2 0.2 + - - -
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Residues in contact with PHE 190 (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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181A SER* 3.9 7.6 - - - -
186A TYR* 3.4 41.1 - + - -
188A GLY 4.1 0.4 + - - -
189A ASN* 1.3 80.5 - - - +
191A HIS* 1.3 64.3 + - - +
192A TYR* 3.6 40.3 - - + +
324A TYR* 3.5 41.3 - + - -
326A GLU* 3.9 22.7 - - + -
335A GLY* 3.6 11.2 - - - -
336A PHE 3.3 16.6 - - - +
337A ALA* 3.7 11.4 - - + -
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Residues in contact with HIS 191 (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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189A ASN* 3.4 38.1 + - + +
190A PHE* 1.3 76.5 + - - +
192A TYR* 1.3 63.9 + - - +
193A ILE* 4.1 3.6 - - - +
272A LEU 6.1 0.2 - - - +
273A GLY 5.7 3.6 - - - +
275A LYS* 4.9 15.0 - - + +
277A TYR* 3.6 25.3 + + - +
334A ILE 3.9 0.9 - - - +
335A GLY* 3.7 0.7 - - - -
336A PHE 2.9 28.7 + - - -
337A ALA* 6.0 0.2 - - - -
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Residues in contact with TYR 192 (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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190A PHE* 3.6 36.8 - - + +
191A HIS* 1.3 74.6 - - - +
193A ILE* 1.3 66.1 + - - +
194A ASN* 4.3 2.7 - - - +
273A GLY* 4.5 8.5 - - - +
326A GLU* 3.3 30.0 + - - -
328A ASP* 5.3 0.2 - - + -
333A ARG* 3.4 62.8 + - + +
334A ILE 3.3 4.5 - - - +
335A GLY* 3.4 23.6 - - - -
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Residues in contact with ILE 193 (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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191A HIS 4.1 5.6 - - - +
192A TYR* 1.3 79.9 - - - +
194A ASN* 1.3 76.5 + - - +
195A LEU 3.8 0.2 + - - -
203A ILE* 3.8 24.4 - - + +
204A GLN* 4.3 14.8 - - + +
272A LEU* 3.9 17.9 - - + +
273A GLY* 3.6 30.3 - - - +
277A TYR* 4.3 2.9 - - - +
333A ARG* 4.1 1.8 - - - -
334A ILE 2.9 32.8 + - - +
336A PHE* 3.6 37.0 - - + -
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Residues in contact with ASN 194 (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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192A TYR* 5.4 2.3 - - - +
193A ILE* 1.3 83.4 + - - +
195A LEU* 1.3 68.4 + - - +
196A ILE* 3.8 1.0 + - - +
203A ILE* 3.4 11.6 - - - +
204A GLN* 4.7 2.1 + - - +
331A ASN 4.9 3.1 - - - +
332A ASN 3.8 8.7 - - - +
333A ARG* 4.0 14.8 + - - +
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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