Contacts of the strand formed by residues 190 - 195 (chain B) in PDB entry 5GQQ
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 ASN 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B SER* 3.3 3.5 - - - -
142B PHE* 3.0 44.3 + - + -
144B GLY 2.9 25.2 + - - +
145B PHE* 3.9 3.0 - - - +
146B SER* 3.1 34.3 + - - +
177B ALA 3.5 4.9 - - - +
178B GLY* 3.2 24.9 - - - -
179B TYR* 3.7 4.4 + - - -
180B ASN* 4.3 11.8 + - - +
181B SER* 3.8 14.6 + - - -
188B ARG 3.9 0.2 + - - -
189B ASN* 1.3 77.5 - - - +
191B GLU* 1.3 59.1 + - - +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ARG* 2.8 26.3 + - - -
139B VAL* 3.5 18.0 - - + +
140B ARG 3.3 9.6 - - - +
141B SER* 4.3 11.4 - - - -
142B PHE* 3.7 5.8 - - - -
176B THR* 3.3 5.7 - - - -
177B ALA* 2.9 30.6 + - + +
179B TYR* 2.9 33.9 + - + -
188B ARG* 3.9 6.2 + - - -
189B ASN 3.6 8.5 - - - +
190B ASN* 1.3 81.5 - - - +
192B VAL* 1.3 63.2 + - - +
193B TRP* 2.9 24.5 + - - +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B PHE 3.8 0.7 - - - +
139B VAL* 3.6 0.2 - - - -
140B ARG* 3.0 46.9 + - + +
142B PHE* 4.0 5.8 - - + -
151B ASN* 3.9 41.7 - - + +
154B GLN* 4.2 5.2 - - + -
155B LEU* 4.0 38.1 - - + +
158B LEU* 4.3 3.0 - - + +
174B TYR* 4.9 0.4 - - + -
175B TYR 3.4 11.9 - - - +
176B THR* 4.5 3.8 - - + -
191B GLU* 1.3 74.9 - - - +
193B TRP* 1.3 67.6 + - - +
194B LEU 4.4 0.2 - - - -
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Residues in contact with TRP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PRO* 5.6 0.4 - - + -
41B ARG* 4.3 0.9 - - - -
43B TYR* 3.4 35.0 - + - -
48B TRP* 5.3 4.0 - + - -
88B PRO* 4.7 4.5 - - + -
90B THR* 4.0 20.0 - - + -
132B ARG* 4.6 4.0 - - - -
135B MET* 3.9 18.6 - - + -
137B VAL* 3.9 31.0 - - + -
138B PHE 3.3 4.7 - - - -
139B VAL* 3.6 18.6 - - + +
155B LEU* 4.6 0.9 - - - -
174B TYR* 3.4 11.0 - - - +
175B TYR* 2.9 65.2 + + + -
177B ALA* 3.8 20.9 - - + +
179B TYR* 4.4 3.1 - - - -
191B GLU* 2.9 27.8 + - + +
192B VAL* 1.3 83.8 - - - +
194B LEU* 1.3 61.5 + - - +
195B ILE 4.3 0.2 + - - -
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Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B VAL* 3.3 3.4 - - - -
138B PHE* 2.8 34.1 + - - -
155B LEU* 3.6 26.2 - - + -
158B LEU* 3.7 15.8 - - + +
159B ALA* 3.9 26.2 - - + +
162B LEU* 3.7 29.4 - - + -
169B PHE* 4.1 14.8 - - + -
170B ASP 4.0 5.8 - - - +
173B VAL 4.3 0.9 - - - +
174B TYR* 4.2 4.7 - - + -
193B TRP* 1.3 74.6 - - - +
195B ILE* 1.3 62.7 + - - +
57D TRP* 3.5 34.5 - - + +
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Residues in contact with ILE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B TYR* 4.1 6.3 - - + +
135B MET* 4.7 15.7 - - + -
136B THR 3.8 9.9 - - - +
137B VAL* 4.0 14.8 - - + -
169B PHE* 3.1 4.2 - - - +
170B ASP* 2.8 42.7 + - + +
173B VAL* 3.8 32.6 + - + +
174B TYR* 5.1 0.2 - - - -
175B TYR* 3.8 30.5 - - + +
193B TRP 5.1 1.1 - - - +
194B LEU* 1.3 76.0 - - - +
196B GLN* 1.3 72.7 + - - +
197B LYS* 6.0 0.4 - - + -
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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