Contacts of the strand formed by residues 171 - 176 (chain D) in PDB entry 1U3H
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 171 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LEU* 3.7 15.3 - - + -
131D TRP* 3.8 15.7 - - + -
132D PHE 3.2 10.8 - - - +
133D ARG* 3.8 25.5 + - + -
138D GLU* 5.5 0.2 - - - -
161D LEU* 3.6 31.4 - - + -
163D MET* 3.6 40.6 - - + +
164D THR 3.8 4.9 + - - -
165D PRO* 4.9 1.1 - - + -
169D GLU* 2.9 46.1 + - + -
170D VAL* 1.3 76.4 - - - +
172D THR* 1.3 62.7 + - - +
187D GLU* 3.3 5.0 - - - +
188D TRP* 2.9 52.1 + + + +
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Residues in contact with THR 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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130D ARG 3.7 1.0 - - - +
131D TRP* 3.1 12.6 - - - -
132D PHE* 2.8 48.8 + - + +
135D GLY 6.3 0.4 - - - -
170D VAL* 4.3 6.5 + - - +
171D TYR* 1.3 78.8 + - - +
173D CYS* 1.3 72.1 + - - +
174D HIS* 4.4 1.3 - - + +
185D THR* 4.0 23.1 - - + -
186D VAL 3.1 9.9 - - - +
187D GLU* 3.5 17.6 + - + +
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Residues in contact with CYS 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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99D VAL* 4.1 9.3 - - + +
101D ILE* 3.9 17.0 - - + +
117D CYS* 2.0 51.8 - - + -
129D VAL* 3.7 21.8 - - - -
130D ARG 3.5 4.9 - - - -
131D TRP* 4.4 6.3 - - + -
172D THR* 1.3 72.8 - - - +
174D HIS* 1.3 59.4 + - - +
175D VAL* 4.2 2.6 - - - +
184D ILE 3.4 1.4 - - - +
185D THR* 3.1 6.4 - - - -
186D VAL* 2.8 33.2 + - + +
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Residues in contact with HIS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LYS* 3.5 2.2 - - + +
129D VAL* 3.2 5.4 - - - -
130D ARG* 2.8 56.0 + - + +
132D PHE* 3.8 26.1 - + + -
172D THR* 4.0 1.1 - - + -
173D CYS* 1.3 72.7 - - - +
175D VAL* 1.3 65.2 + - - +
176D GLU* 3.0 32.7 + - + -
183D PRO* 3.5 25.7 - - + +
184D ILE 3.4 1.3 + - - -
185D THR* 3.1 26.9 - - + +
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Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D PRO* 4.4 11.9 - - + -
99D VAL* 3.9 24.7 - - + -
119D VAL* 3.9 19.7 - - + -
127D ILE* 3.9 28.3 - - + -
128D LYS 3.2 4.3 - - - +
129D VAL* 3.8 20.6 - - + -
173D CYS* 4.2 2.5 - - - -
174D HIS* 1.3 79.4 - - - +
176D GLU* 1.3 68.9 + - - +
180D LEU* 4.1 6.6 - - + +
183D PRO* 3.3 5.8 - - - +
184D ILE* 2.8 39.9 + - + +
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Residues in contact with GLU 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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127D ILE* 3.5 4.9 - - - +
128D LYS* 2.9 62.4 + - + +
130D ARG* 3.4 10.7 + - - -
174D HIS* 3.0 24.8 + - + +
175D VAL* 1.3 73.6 - - - +
177D HIS* 1.3 62.5 + - - +
183D PRO* 3.5 31.2 - - + +
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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