Contacts of the strand formed by residues 162 - 165 (chain D) in PDB entry 1W4R
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 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A PRO 3.3 21.1 - - - -
142A LEU 2.7 27.5 + - - -
143A ALA 4.1 2.0 - - - -
144A GLU* 2.9 26.9 + - + -
27D PRO* 3.5 7.5 - - - +
130D ARG* 3.1 38.8 - - + -
161D ALA* 1.3 103.6 - - + +
163D THR* 1.3 64.5 + - - +
183D SER* 3.3 6.2 - - - -
184D VAL* 2.9 45.5 + - + +
185D CYS* 3.8 2.9 - - - -
186D ARG* 3.2 36.4 + - + -
189D TYR* 4.2 6.5 - - + -
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Residues in contact with THR 163 (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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27D PRO* 3.6 4.3 - - - +
28D MET* 3.0 59.3 + - + +
124D LEU* 4.5 1.7 - - - +
126D GLY 5.0 2.7 + - - -
127D THR 4.2 4.7 + - - +
128D PHE* 3.5 25.1 - - - +
130D ARG* 5.4 0.6 - - - +
162D TYR* 1.3 75.0 - - - +
164D LYS* 1.3 61.0 + - - +
181D TYR* 3.8 16.4 - - + -
182D HIS 3.6 7.0 - - - +
183D SER 4.9 0.2 - - - +
184D VAL* 4.4 2.0 - - - -
189D TYR* 3.7 6.5 - - - -
300D TTP 3.7 20.0 - - + +
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Residues in contact with LYS 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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128D PHE 4.9 0.2 - - - -
155D GLU* 2.8 39.2 + - - +
163D THR* 1.3 72.6 - - - +
165D ARG* 1.3 71.8 + - - +
166D LEU* 3.8 11.7 + - + +
181D TYR* 3.2 8.6 - - - +
182D HIS* 2.8 38.4 + - + +
184D VAL* 3.8 13.4 - - + +
188D CYS 3.0 24.9 + - - -
189D TYR* 3.8 24.4 + - + +
191D LYS* 4.8 11.4 + - - +
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Residues in contact with ARG 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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128D PHE* 3.3 53.8 + - + +
164D LYS* 1.3 83.3 - - - +
166D LEU* 1.3 62.6 + - - +
167D GLY 3.7 20.2 - - - +
169D GLU* 2.8 46.2 + - - +
171D GLU 2.7 21.4 + - - -
172D VAL 3.0 26.7 + - - -
174D VAL* 3.5 14.4 - - - +
180D LYS 3.7 9.2 - - - +
181D TYR* 3.0 30.4 + - + -
300D TTP 3.8 1.0 + - - -
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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