Contacts of the strand formed by residues 171 - 176 (chain D) in PDB entry 1XHU
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 VAL 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D LEU* 4.4 15.7 - - + -
37D PHE* 3.8 35.7 - - + -
41D VAL* 4.6 5.8 - - + -
128D VAL* 4.2 12.8 - - + -
129D LYS 2.8 11.0 + - - +
130D THR* 3.5 9.3 - - + -
131D ARG 3.2 16.5 + - - -
169D LEU* 3.2 26.2 - - + +
170D GLU* 1.3 73.7 - - - +
172D ASP* 1.3 64.4 + - - +
173D TRP* 3.4 7.8 - - - -
182D CYS* 4.0 19.1 - - + -
184D SER 3.8 2.7 - - - -
185D THR* 4.8 0.9 - - + -
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Residues in contact with ASP 172 (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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131D ARG* 3.0 36.8 - - - +
133D ILE* 3.5 17.5 - - + -
170D GLU* 3.8 17.5 - - - +
171D VAL* 1.3 71.3 - - - +
173D TRP* 1.3 54.9 + - - +
182D CYS* 3.1 9.9 - - - -
183D VAL* 2.7 47.7 + - + -
184D SER* 2.9 26.6 + - - +
185D THR* 5.1 0.2 - - - -
186D SER* 4.7 1.9 + - - -
213D ARG* 3.5 16.7 + - - -
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Residues in contact with TRP 173 (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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28D LEU* 4.5 14.8 - - + -
33D ALA* 3.9 24.7 - - + -
34D GLY* 4.3 4.2 - - - -
37D PHE* 3.6 30.5 - + + -
130D THR* 3.6 19.6 - - - -
131D ARG 3.0 30.7 + - - -
132D ASN* 2.9 34.1 - - - +
133D ILE* 3.0 26.2 + - - +
171D VAL 3.4 13.5 - - - -
172D ASP* 1.3 73.4 - - - +
174D GLU* 1.3 65.4 + - - +
175D LEU* 4.4 5.4 - - + -
180D LEU* 3.4 46.0 - - + -
181D VAL 3.1 13.9 - - - +
183D VAL* 4.3 0.9 - - - +
10J C 3.5 12.1 - - - -
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Residues in contact with GLU 174 (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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132D ASN* 4.9 0.4 - - - -
133D ILE* 3.4 18.3 - - + +
134D SER* 3.6 14.3 + - - +
173D TRP* 1.3 85.9 - - - +
175D LEU* 1.3 58.9 + - - +
176D ASN* 3.0 29.0 + - + +
180D LEU* 4.2 0.7 - - - -
181D VAL* 3.0 28.3 + - + +
183D VAL* 4.1 18.5 - - + +
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Residues in contact with LEU 175 (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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22D ARG* 3.5 21.8 - - + +
28D LEU* 3.4 33.0 - - + -
132D ASN* 5.4 0.6 + - - -
134D SER* 4.4 5.1 + - - -
173D TRP* 4.2 4.8 - - + -
174D GLU* 1.3 69.7 - - - +
176D ASN* 1.3 57.4 + - - +
177D GLY 3.3 28.2 + - - +
178D GLU 3.7 11.7 - - - +
179D ASP 3.4 16.6 - - - +
180D LEU* 3.4 22.8 - - + +
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Residues in contact with ASN 176 (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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174D GLU* 3.0 28.4 + - + +
175D LEU* 1.3 68.9 - - - +
177D GLY* 1.3 59.5 + - - +
178D GLU 3.4 5.9 + - - -
179D ASP* 3.2 13.9 + - - +
181D VAL* 4.8 13.7 - - + +
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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