Contacts of the strand formed by residues 190 - 195 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A SER* 3.3 3.8 - - - -
142A PHE* 3.1 43.7 + - + -
144A GLY 3.0 22.6 + - - +
146A SER* 3.4 27.1 + - - +
177A ALA 3.4 7.4 - - - +
178A GLY* 3.4 2.8 - - - -
179A TYR* 2.6 26.4 + - - +
180A ASN* 2.5 39.8 + - - +
181A SER* 3.7 3.5 - - - -
189A ASN* 1.3 75.8 - - - +
191A GLU* 1.3 59.4 + - - +
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ARG* 2.7 26.9 + - - -
139A VAL* 3.5 16.6 - - + +
140A ARG 3.3 7.0 - - - +
141A SER* 4.1 12.6 - - - -
142A PHE* 3.8 6.5 - - - -
151A ASN* 5.2 0.2 - - - +
176A THR* 3.5 4.9 - - - -
177A ALA* 2.9 31.7 + - + +
179A TYR* 2.9 27.0 + - + -
188A ARG* 3.1 13.2 + - - -
189A ASN 3.9 5.9 - - - +
190A ASN* 1.3 80.9 - - - +
192A VAL* 1.3 66.3 + - - +
193A TRP* 2.9 28.3 + - + +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A PHE 3.7 1.2 - - - +
139A VAL* 3.6 0.3 - - - -
140A ARG* 3.0 43.9 + - + +
142A PHE* 3.9 13.0 - - + -
151A ASN* 3.8 34.1 - - + +
154A GLN* 4.0 10.5 - - + +
155A LEU* 3.8 38.1 - - + +
158A LEU* 4.2 3.1 - - + +
174A TYR* 5.1 0.7 - - + -
175A TYR 3.4 9.2 - - - +
176A THR* 4.5 3.6 - - + -
191A GLU* 1.3 77.9 - - - +
193A TRP* 1.3 66.5 + - - +
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Residues in contact with TRP 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PRO* 5.6 0.2 - - + -
41A ARG* 4.2 0.2 - - - -
43A TYR* 3.5 35.2 - + - -
48A TRP* 5.1 3.4 - + - -
88A PRO* 4.5 5.8 - - + -
90A THR* 4.0 24.2 - - + -
132A ARG* 4.4 4.9 - - - -
135A MET* 4.0 17.9 - - + -
137A VAL* 4.0 25.4 - - + -
138A PHE 3.2 6.5 - - - +
139A VAL* 3.5 23.0 - - + +
155A LEU* 4.6 0.9 - - - -
174A TYR* 3.3 10.7 - - - +
175A TYR* 2.7 65.9 + + + -
177A ALA* 3.6 20.8 - - + +
179A TYR* 4.3 3.4 - - - -
191A GLU* 2.9 29.5 + - + +
192A VAL* 1.3 82.5 - - - +
194A LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 3.2 4.0 - - - -
138A PHE* 2.6 38.9 + - - +
155A LEU* 3.6 25.4 - - + -
158A LEU* 3.6 15.2 - - + +
159A ALA* 4.1 24.0 - - + +
162A LEU* 3.6 30.3 - - + -
169A PHE* 4.2 13.7 - - + -
170A ASP 4.1 6.1 - - - +
173A VAL 4.3 0.9 - - - +
174A TYR* 4.0 7.9 - - + -
193A TRP* 1.3 71.9 - - - +
195A ILE* 1.3 62.2 + - - +
57C TRP* 3.5 37.7 - - + +
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Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR* 4.0 5.4 - - + +
135A MET* 4.8 13.2 - - + -
136A THR 3.7 10.1 - - - +
137A VAL* 4.2 8.5 - - + -
138A PHE* 4.6 0.4 - - - -
169A PHE* 3.2 5.1 - - - +
170A ASP* 2.9 38.6 + - + +
173A VAL* 3.8 30.6 + - + +
174A TYR* 5.1 2.9 - - - -
175A TYR* 3.6 36.8 - - + -
193A TRP 5.1 0.7 - - - +
194A LEU* 1.3 77.9 - - - +
196A GLN* 1.3 73.8 + - - +
197A 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