Contacts of the strand formed by residues 163 - 170 (chain D) in PDB entry 5YL4
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 163 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407C TRP* 4.7 5.4 - - + -
1D MET* 4.8 0.4 - - + -
131D GLN 3.1 14.4 + - - +
132D GLY* 3.3 0.9 - - - -
133D PHE* 2.8 35.7 + - - +
162D ARG* 1.3 73.4 - - - +
164D MET* 1.3 64.1 + - - +
165D ASN 4.4 2.0 - - - +
197D ASP* 3.3 25.1 - - + +
198D GLU* 3.9 15.7 - - + +
250D LEU* 3.8 26.9 - - + +
251D ARG* 3.6 59.0 - - + +
254D ALA* 4.6 6.3 - - + -
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Residues in contact with MET 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 6.3 0.9 - - - -
133D PHE* 3.8 26.0 - - + +
135D LEU* 5.2 4.7 - - - -
152D ILE* 3.9 35.0 - - + +
155D ILE* 3.7 40.4 - - + -
156D ARG* 3.8 22.9 - - - +
162D ARG 3.8 0.4 + - - +
163D ILE* 1.3 73.6 - - - +
165D ASN* 1.3 64.8 + - - +
166D THR* 4.7 1.6 - - + -
195D ASN 4.0 4.9 - - - +
196D THR* 3.5 24.7 - - + -
197D ASP* 2.9 31.8 + - - -
198D GLU 3.4 4.3 + - - -
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Residues in contact with ASN 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PHE 2.8 16.1 + - - +
134D GLN* 3.1 18.1 + - + +
135D LEU 3.1 21.1 + - - -
163D ILE* 3.9 1.8 - - + -
164D MET* 1.3 76.0 - - - +
166D THR* 1.3 67.2 + - - +
167D PHE* 3.7 25.5 - - - -
198D GLU* 3.0 29.0 - - + +
200D TYR* 3.2 30.2 + - - -
237D THR* 6.0 0.6 - - - +
240D LEU* 5.8 1.4 - - - +
250D LEU* 4.1 26.3 - - + +
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Residues in contact with THR 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 3.5 15.0 - - + -
137D HIS* 4.0 4.5 - - - +
152D ILE* 3.8 20.6 - - + -
164D MET* 4.7 2.2 - - + -
165D ASN* 1.3 80.0 + - - +
167D PHE* 1.3 65.3 + - - +
168D SER* 2.9 19.7 + - - -
192D LEU* 4.1 2.0 - - + +
196D THR* 3.7 25.4 - - + -
198D GLU 2.9 8.9 + - - -
199D THR* 2.7 24.3 + - - +
200D TYR* 2.9 32.9 + - - -
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Residues in contact with PHE 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 4.3 2.8 - - + +
20D PHE* 6.1 0.2 - + - -
134D GLN* 3.8 26.0 - - + -
135D LEU 2.9 19.2 + - - +
136D THR* 3.9 19.0 - - + -
137D HIS* 3.1 26.6 + - - +
165D ASN* 3.7 25.1 - - - -
166D THR* 1.3 71.9 - - - +
168D SER* 1.3 59.5 + - - +
169D VAL* 3.6 4.2 + - - +
200D TYR* 3.6 27.4 - + + -
202D ILE* 3.7 28.5 - - + -
232D THR* 5.8 2.0 - - + -
233D MET* 3.8 26.2 - - + -
236D VAL* 3.6 27.8 - - + -
237D THR* 4.4 8.5 - - + -
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Residues in contact with SER 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D HIS* 2.7 30.4 + - - -
139D LEU* 3.8 22.0 - - - -
166D THR* 2.9 18.8 + - - -
167D PHE* 1.3 70.4 - - - +
169D VAL* 1.3 62.6 + - - +
170D MET* 3.6 6.2 + - - +
192D LEU* 3.7 5.9 - - - +
199D THR* 3.4 18.1 - - - +
200D TYR 3.2 7.8 + - - +
201D CYS* 3.9 3.3 - - - -
202D ILE 3.3 19.4 + - - -
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Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D CYS* 3.7 28.0 - - - -
16D ILE* 3.9 17.7 - - + -
137D HIS 2.8 22.4 + - - +
138D SER* 3.4 6.9 - - - +
139D LEU* 3.0 26.1 + - - +
140D GLY 4.2 0.3 + - - -
167D PHE 4.3 1.3 - - - +
168D SER* 1.3 70.8 - - - +
170D MET* 1.3 64.8 + - - +
171D PRO* 3.8 1.0 - - - +
202D ILE* 3.2 26.9 - - + +
204D ASN* 3.5 37.7 - - - +
501D GTP 3.9 4.7 - - - +
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Residues in contact with MET 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LEU* 3.5 30.3 - - + -
168D SER* 4.0 9.4 - - - +
169D VAL* 1.3 73.6 - - - +
171D PRO* 1.3 70.2 - - + +
185D ALA* 4.7 4.3 - - + -
189D VAL* 4.7 10.8 - - + -
199D THR* 6.3 0.2 - - - -
201D CYS* 4.5 13.5 - - + -
202D ILE 2.9 15.0 + - - +
203D ASP* 3.6 18.5 - - - +
204D ASN* 3.1 26.9 + - - +
377D LEU* 3.6 40.2 - - + -
378D PHE* 4.9 1.6 - - + -
380D ARG* 4.4 4.9 - - - +
381D ILE* 4.1 22.7 - - + -
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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