Contacts of the helix formed by residues 191 - 202 (chain A) in PDB entry 1XUQ
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 ASP 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A THR 4.7 1.6 - - - +
89A ILE* 2.8 27.1 + - - +
90A LEU 4.1 2.4 - - - +
91A SER* 3.6 28.3 + - - -
93A ASN* 5.3 3.2 - - - +
94A GLY* 4.3 7.2 - - - -
189A VAL 3.4 0.2 + - - -
190A VAL* 1.3 72.0 - - - +
192A TRP* 1.3 57.9 + - - +
193A ASN* 3.0 15.5 + - - +
194A ALA* 3.0 30.1 + - + +
195A ALA* 3.0 25.7 + - - +
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Residues in contact with TRP 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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94A GLY* 5.3 1.0 - - - -
95A GLY 3.6 15.8 + - - +
96A GLY 3.3 26.3 + - - -
97A GLN 3.8 14.1 - - - +
98A PRO* 3.7 20.4 - - + -
99A VAL* 3.7 12.8 + - + +
102A LEU* 4.0 14.0 - - + +
106A ILE* 3.9 20.2 - - + -
113A PHE* 3.5 28.0 - + - -
116A PHE* 3.9 14.1 - + - -
135A LEU* 4.9 2.0 - - + -
162A ILE* 3.9 29.4 - - + -
187A TRP* 4.1 9.6 + + - -
190A VAL* 3.3 34.0 + - + +
191A ASP* 1.3 70.5 + - - +
193A ASN* 1.3 60.3 + - - +
194A ALA 3.3 0.2 - - - -
195A ALA* 3.7 13.4 - - + +
196A GLU* 2.9 28.8 + - - +
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Residues in contact with ASN 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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93A ASN* 4.7 14.1 - - - +
99A VAL* 3.5 26.0 - - - +
191A ASP* 3.0 9.5 + - - +
192A TRP* 1.3 78.6 - - - +
194A ALA* 1.3 60.9 + - - +
196A GLU* 3.3 5.3 + - - +
197A LYS* 3.2 20.8 + - - +
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Residues in contact with ALA 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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88A THR 3.5 22.9 - - - +
89A ILE* 4.5 7.0 - - + -
191A ASP* 3.0 31.2 + - + +
193A ASN* 1.3 73.8 - - - +
195A ALA* 1.3 64.3 - - - +
197A LYS* 3.2 10.7 + - - +
198A ARG* 3.2 25.9 + - - +
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Residues in contact with ALA 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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89A ILE* 5.0 2.2 - - + +
102A LEU* 3.7 17.5 - - + -
161A VAL* 3.6 16.6 - - - +
162A ILE* 3.5 30.1 - - + -
191A ASP 3.0 14.5 + - - +
192A TRP* 3.7 11.0 - - + +
194A ALA* 1.3 73.1 - - - +
196A GLU* 1.3 67.1 + - - +
198A ARG* 3.2 2.7 + - - +
199A TYR* 3.0 23.7 + - - +
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Residues in contact with GLU 196 (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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99A VAL* 3.6 13.7 - - + +
100A GLY* 3.5 11.5 - - - -
101A GLU* 2.8 24.6 + - - +
102A LEU* 2.8 33.8 + - - +
192A TRP 2.9 14.9 + - - +
193A ASN* 3.4 11.0 - - - +
194A ALA 3.3 0.2 - - - -
195A ALA* 1.3 76.1 - - - +
197A LYS* 1.3 58.8 + - - +
199A TYR* 3.2 4.7 + - - +
200A GLN* 2.8 58.4 + - + +
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Residues in contact with LYS 197 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A ASN 3.2 9.3 + - - +
194A ALA* 3.5 11.9 - - - +
195A ALA 3.2 0.4 - - - -
196A GLU* 1.3 80.3 - - - +
198A ARG* 1.3 58.1 + - + +
200A GLN* 3.4 9.2 + - + +
201A GLU* 2.8 65.5 + - - +
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Residues in contact with ARG 198 (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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84A THR* 6.2 0.8 - - - +
85A PHE* 3.4 45.6 - - - +
88A THR* 2.9 33.1 + - - +
89A ILE* 4.0 9.8 - - - +
159A THR* 4.7 3.2 - - + +
160A PRO* 4.1 13.0 + - - +
161A VAL* 4.1 14.5 - - - +
194A ALA* 3.2 12.9 + - - +
195A ALA 3.2 6.7 + - - +
197A LYS* 1.3 76.5 - - + +
199A TYR* 1.3 57.8 + - - +
201A GLU* 3.5 11.8 + - - +
202A ALA* 3.1 30.1 + - - +
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Residues in contact with TYR 199 (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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101A GLU* 4.0 20.1 + - + -
102A LEU* 3.8 48.7 - - + -
105A ALA* 3.4 20.1 - - + +
137A VAL* 3.8 27.1 - - + +
140A GLY 5.1 8.1 + - - -
142A LEU* 4.1 15.0 - - + +
161A VAL* 4.4 9.1 - - + +
195A ALA 3.0 13.2 + - - +
196A GLU* 3.2 10.7 + - - +
198A ARG* 1.3 75.8 - - - +
200A GLN* 1.3 70.2 + - - +
202A ALA* 3.3 16.9 + - - +
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Residues in contact with GLN 200 (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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101A GLU* 3.1 41.2 + - - +
196A GLU* 2.8 46.3 + - + +
197A LYS* 3.6 11.4 - - + +
199A TYR* 1.3 82.0 - - - +
201A GLU* 1.3 63.1 + - + +
202A ALA 3.5 2.6 + - - -
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Residues in contact with GLU 201 (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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197A LYS* 2.8 59.3 + - + +
198A ARG* 3.5 10.9 + - - +
199A TYR 3.2 0.2 - - - -
200A GLN* 1.3 78.6 - - + +
202A ALA* 1.3 63.1 + - - +
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Residues in contact with ALA 202 (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* 4.2 27.1 - - + -
159A THR* 3.5 36.3 - - + +
161A VAL* 5.5 0.4 - - + -
198A ARG 3.1 18.4 + - - +
199A TYR* 3.3 11.6 + - - +
200A GLN 3.3 3.2 - - - +
201A GLU* 1.3 81.6 - - - +
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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