Contacts of the strand formed by residues 177 - 181 (chain D) in PDB entry 4QRR
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 THR 177 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ASP* 3.5 3.6 + - + +
176D LYS* 1.3 78.0 - - - +
178D VAL* 1.3 63.2 + - - +
179D LEU 3.8 0.3 + - - -
189D ASN* 3.6 5.9 - - - -
190D SER* 3.2 28.6 + - - -
184E SER* 2.7 22.9 + - - -
185E THR 4.1 4.9 - - - +
186E ASP* 3.6 25.8 - - - +
187E PRO* 3.9 24.0 - - + -
206E ARG* 3.0 23.5 + - - +
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Residues in contact with VAL 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 3.7 34.8 - - + -
130D VAL 4.5 10.5 - - - +
131D HIS* 5.3 2.9 - - - +
132D PRO* 3.8 26.5 - - + -
176D LYS 5.7 0.7 - - - +
177D THR* 1.3 73.1 - - - +
179D LEU* 1.3 67.6 + - - +
180D ASP* 4.2 1.7 + - - +
187D LYS* 4.9 2.2 - - + -
188D SER 4.2 4.3 - - - +
189D ASN* 3.5 18.4 - - - +
183E VAL 4.5 2.4 - - - +
184E SER* 3.6 11.4 + - - -
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Residues in contact with LEU 179 (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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177D THR 3.8 0.8 + - - -
178D VAL* 1.3 75.7 - - - +
180D ASP* 1.3 62.8 + - - +
181D MET* 3.8 19.5 - - + +
186D PHE 5.2 1.1 - - - +
187D LYS* 3.4 26.2 - - - +
188D SER* 3.3 25.9 + - - +
190D SER* 4.7 8.3 - - - +
155E THR* 5.2 2.2 - - + -
182E GLY* 3.4 33.2 - - - +
183E VAL 4.7 1.1 - - - -
184E SER* 3.9 19.3 - - - -
206E ARG* 4.3 14.6 - - + -
208E ARG* 3.7 38.8 - - + +
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Residues in contact with ASP 180 (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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96D LEU* 3.7 19.7 - - + +
97D GLU* 4.7 3.8 - - - +
178D VAL 4.2 1.9 + - - +
179D LEU* 1.3 75.1 - - - +
181D MET* 1.3 56.7 + - - +
182D ARG* 3.6 43.9 + - + +
185D ASP* 6.0 0.5 - - - -
186D PHE 3.9 1.8 - - - -
187D LYS* 3.5 27.2 + - + +
180E HIS 5.8 1.6 - - - +
181E SER* 3.5 8.2 + - - -
182E GLY* 2.6 31.5 + - - +
183E VAL 4.7 4.5 + - - +
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Residues in contact with MET 181 (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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179D LEU* 3.8 8.9 - - + -
180D ASP* 1.3 69.6 + - - +
182D ARG* 1.3 54.4 + - - +
183D SER* 3.3 3.8 - - - +
184D MET* 3.4 12.5 + - + +
185D ASP* 2.8 30.3 + - - -
186D PHE* 2.8 54.6 + - + +
153E LYS* 3.8 17.3 - - + -
181E SER* 3.9 4.0 - - - +
182E GLY* 4.1 10.8 - - - +
208E ARG* 3.7 53.4 - - + +
209E VAL* 4.8 6.5 - - - -
210E SER* 5.3 0.9 - - - -
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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