Contacts of the strand formed by residues 294 - 301 (chain A) in PDB entry 1DS1
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 TRP 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LEU* 4.5 7.0 - - + -
77A PRO* 3.5 44.6 - - + -
78A THR 3.8 4.3 - - - -
79A THR* 3.9 3.6 - - + -
80A PRO* 3.3 34.5 - - + +
89A ARG* 3.9 5.8 - - - -
92A LEU* 3.7 31.0 - - + -
122A ASP* 2.9 30.5 + - + -
123A VAL 3.5 5.4 - - - -
124A TYR* 5.2 0.2 - - + -
162A SER* 3.0 34.9 + - - -
163A ARG* 2.9 40.9 + - + +
292A ASP 3.4 7.8 + - - +
293A ARG* 1.3 76.4 - - - +
295A LEU* 1.3 73.7 + - - +
296A HIS* 3.3 11.3 + - - -
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Residues in contact with LEU 295 (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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122A ASP* 3.5 1.6 - - - -
123A VAL* 2.8 49.2 + - + +
159A LEU* 4.4 13.2 - - + -
160A ALA 3.2 9.0 - - - +
161A CYS* 3.9 29.8 - - + -
163A ARG 4.3 2.2 - - - +
264A LEU* 3.9 18.6 - - + -
293A ARG* 3.7 44.9 - - + +
294A TRP* 1.3 88.8 - - - +
296A HIS* 1.3 65.4 + - - +
330A AKG 3.7 16.6 - - - +
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Residues in contact with HIS 296 (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 LEU* 3.7 18.0 - - + +
94A MET* 4.0 13.3 - - + +
95A GLU* 3.8 25.8 - - + -
98A LEU* 3.6 23.6 - - + +
120A TYR* 5.0 4.3 - + + -
121A HIS 3.4 5.6 - - - +
122A ASP* 3.4 20.0 - - - -
159A LEU* 3.4 4.0 - - - -
160A ALA 2.8 38.7 + - - +
162A SER* 2.7 36.6 + - - -
294A TRP* 3.3 23.9 + + - -
295A LEU* 1.3 73.5 - - - +
297A ARG* 1.3 59.4 + - - +
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Residues in contact with ARG 297 (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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114A LEU* 4.9 0.8 - - - +
115A ARG* 3.9 7.9 - - - +
119A VAL 3.6 2.3 - - - +
120A TYR* 3.7 0.2 - - - -
121A HIS* 2.8 67.3 + - + +
123A VAL* 4.0 10.1 - - + +
134A SER* 3.8 11.3 - - - -
146A GLU* 3.7 4.9 + - - -
157A VAL* 4.1 8.5 - - + -
158A MET 3.3 9.2 - - - +
159A LEU* 3.8 13.5 - - + -
296A HIS* 1.3 74.1 - - - +
298A VAL* 1.3 72.0 + - - +
299A TYR* 3.2 30.6 + - + -
330A AKG 3.0 40.0 + - - -
340A SO4 2.7 37.8 + - - -
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Residues in contact with VAL 298 (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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98A LEU* 4.1 9.2 - - + -
108A HIS* 3.9 24.0 - - + +
119A VAL* 3.8 18.4 - - + +
120A TYR* 3.8 33.2 - - + -
157A VAL* 3.8 2.9 - - - -
158A MET* 3.0 67.3 + - + +
296A HIS 4.3 0.2 - - - -
297A ARG* 1.3 81.3 - - - +
299A TYR* 1.3 67.3 + - - +
300A ILE* 4.2 3.3 + - + -
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Residues in contact with TYR 299 (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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108A HIS* 3.3 6.2 - - - -
109A THR* 2.9 41.5 + - - +
111A TYR* 3.7 21.1 - + + +
114A LEU* 3.8 12.3 - - + +
119A VAL* 4.9 1.9 + - - +
121A HIS* 3.8 25.6 - + - -
146A GLU* 2.7 41.5 + - + +
147A MET* 3.6 15.3 - - + +
154A PRO* 3.9 26.2 - - + -
156A TYR 3.5 2.2 - - - -
157A VAL* 4.0 11.7 - - + -
297A ARG* 3.2 33.8 + - + -
298A VAL* 1.3 80.4 - - - +
300A ILE* 1.3 62.9 + - - +
340A SO4 4.7 0.7 + - - -
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Residues in contact with ILE 300 (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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102A GLY* 3.7 23.6 - - - +
105A LEU* 4.1 3.4 - - + -
106A GLY* 3.7 31.2 - - - +
107A LEU 3.5 1.8 - - - +
108A HIS* 3.8 30.5 - - + +
154A PRO* 3.7 1.5 - - - +
155A ASN* 3.1 23.9 + - - +
156A TYR* 3.0 35.9 + - + -
158A MET* 3.8 31.9 - - + -
298A VAL* 4.2 1.3 - - + -
299A TYR* 1.3 79.9 - - - +
301A ARG* 1.3 66.3 + - - +
302A THR* 4.5 0.2 - - + -
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Residues in contact with ARG 301 (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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106A GLY* 3.3 6.2 - - - -
107A LEU* 2.8 39.3 + - + +
109A THR* 2.9 38.1 + - - +
111A TYR* 4.2 7.9 - - - +
152A LEU* 4.1 22.9 - - - +
154A PRO* 4.3 4.5 - - + -
300A ILE* 1.3 75.0 - - - +
302A THR* 1.3 60.9 - - - +
307A GLN* 3.0 43.9 + - - +
308A LEU* 3.8 20.3 - - + +
312A GLU* 3.7 27.7 + - - +
313A ARG 5.1 2.0 + - - -
316A ASP* 4.4 11.9 - - - +
318A VAL* 3.6 27.5 - - - +
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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