Contacts of the strand formed by residues 134 - 138 (chain A) in PDB entry 6U17
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 ILE 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.5 2.1 - - - +
133A ASP* 1.3 86.3 - - + +
135A VAL* 1.3 68.1 + - - +
136A ILE* 3.7 31.6 - - + -
168A LEU* 4.4 12.3 - - + -
186A GLY 3.0 4.8 + - - +
187A ILE* 3.3 26.2 - - + -
188A GLY 2.8 24.3 + - - -
224A PRO* 4.5 0.9 - - - -
226A ILE* 3.4 18.8 - - + -
228A VAL* 3.9 11.9 - - + -
292A LEU* 4.1 26.0 - - + -
296A ARG* 4.3 26.2 - - + +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.7 26.5 - - + -
132A LEU* 3.7 19.7 - - + -
134A ILE* 1.3 77.8 - - - +
136A ILE* 1.3 63.2 + - - +
137A ILE* 3.5 8.1 + - + +
188A GLY* 3.5 4.9 - - - +
190A THR* 3.9 23.3 - - + +
219A LEU* 4.6 9.2 - - + -
222A TYR* 5.8 1.6 - - + -
224A PRO* 3.5 35.0 - - + -
226A ILE 3.0 9.2 + - - +
227A ALA* 5.0 0.4 - - - -
228A VAL* 2.9 27.5 + - - +
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Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ILE* 3.7 19.7 - - + -
135A VAL* 1.3 70.3 - - - +
137A ILE* 1.3 62.6 + - - +
138A GLY 3.8 0.3 + - - -
152A TYR* 3.6 31.6 + - + +
159A PHE* 3.9 27.8 - - + -
163A LEU* 5.6 3.1 - - + -
168A LEU* 6.5 0.4 - - + -
187A ILE* 3.8 22.9 - - + -
188A GLY 2.8 14.1 + - - +
189A PHE* 3.4 9.3 - - + +
190A THR 3.0 25.5 + - - +
228A VAL* 3.8 19.3 - - + +
230A ASN* 4.1 14.4 - - + +
269A MET* 5.1 4.9 - - + -
289A TYR* 5.7 1.1 - - + -
292A LEU* 4.7 7.4 - - + -
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Residues in contact with ILE 137 (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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135A VAL* 4.0 8.5 - - + +
136A ILE* 1.3 73.2 - - - +
138A GLY* 1.3 72.2 + - - +
190A THR* 3.3 17.9 - - + -
191A ASN* 4.2 3.8 - - - -
192A MET* 3.9 12.3 - - - +
215A LEU* 3.9 26.0 - - + -
219A LEU* 4.2 8.7 - - + -
227A ALA* 3.9 28.3 - - + -
228A VAL 2.7 18.4 + - - +
229A PHE* 3.9 25.1 - - + -
230A ASN* 2.8 29.4 + - - -
234A ILE* 3.4 12.8 - - + +
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Residues in contact with GLY 138 (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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137A ILE* 1.3 76.3 - - - +
139A ILE* 1.3 55.5 + - - -
152A TYR* 3.4 19.4 + - - -
190A THR 3.0 12.5 + - - -
191A ASN* 3.0 13.7 + - - -
192A MET 2.8 27.5 + - - -
230A ASN* 4.1 7.4 - - - -
234A ILE* 3.4 8.5 - - - +
17D 1FC 3.6 4.7 - - - -
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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