Contacts of the strand formed by residues 280 - 285 (chain A) in PDB entry 1DGD
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 LEU 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 3.9 11.4 - - + -
107A LEU* 4.6 14.6 - - + -
108A LEU 3.5 11.2 - - - +
109A SER 3.3 3.2 + - - +
271A SER* 3.2 22.5 - - - +
274A LEU* 3.8 26.3 - - + +
275A GLY* 4.0 12.3 + - - -
278A LEU* 2.9 7.4 + - + +
279A PRO* 1.3 75.8 - - - +
281A ALA* 1.3 78.2 + - - +
310A PRO* 3.4 39.7 - - + +
311A ALA 4.5 2.0 - - - +
313A VAL* 5.7 0.7 - - + -
314A GLY* 3.5 24.0 - - - +
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Residues in contact with ALA 281 (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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107A LEU* 3.6 2.8 - - - -
108A LEU* 2.9 32.7 + - + +
109A SER 3.9 0.2 - - - -
110A THR 3.4 34.8 - - - +
114A SER* 4.1 3.1 - - - -
270A LEU 3.2 16.4 - - - +
271A SER* 3.5 8.5 - - - +
274A LEU* 4.4 4.3 - - - -
280A LEU* 1.3 81.7 - - - +
282A ALA* 1.3 67.2 + - - +
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Residues in contact with ALA 282 (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 LEU* 4.2 17.7 - - + -
106A LEU 3.0 14.4 - - - +
107A LEU* 3.9 15.3 - - + -
108A LEU* 4.4 2.0 - - - +
114A SER* 3.9 4.4 - - - -
268A LEU 4.0 0.2 - - - +
269A THR* 3.4 3.3 - - - -
270A LEU* 2.9 36.1 + - + +
274A LEU* 4.2 9.2 - - + -
281A ALA* 1.3 82.7 - - - +
283A ILE* 1.3 68.9 + - - +
284A VAL* 5.2 0.7 - - - -
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Residues in contact with ILE 283 (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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104A ARG 3.7 0.6 - - - +
105A ALA* 3.1 7.4 - - - +
106A LEU* 3.0 47.2 + - + +
108A LEU* 4.7 2.2 - - + -
114A SER* 3.2 35.0 - - - +
117A ALA* 4.3 11.2 - - + -
118A ALA* 4.2 21.3 - - + +
121A MET* 4.0 29.8 - - + -
267A ILE* 4.2 11.7 - - + -
268A LEU 3.3 7.2 - - - +
269A THR* 4.0 7.6 - - + -
282A ALA* 1.3 78.5 - - - +
284A VAL* 1.3 64.2 + - - +
285A THR* 5.2 4.3 - - + +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.4 32.1 - - + +
95A ALA* 5.0 0.2 - - - -
98A THR* 4.5 9.4 - - + +
102A LEU* 3.3 37.3 - - + +
103A ASP 4.7 1.1 - - - -
104A ARG 3.2 18.6 - - - +
105A ALA* 4.4 4.0 - - + -
267A ILE* 3.6 1.2 - - - -
268A LEU* 2.9 45.5 + - + +
270A LEU* 4.4 15.7 - - + -
283A ILE* 1.3 80.7 - - - +
285A THR* 1.3 59.2 + - - +
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Residues in contact with THR 285 (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 GLY 4.1 2.0 - - - -
102A LEU* 3.9 2.9 - - - -
103A ASP 2.7 28.8 + - - -
104A ARG* 2.8 23.9 + - + +
121A MET* 3.9 26.5 - - + -
266A ASP 2.6 24.0 + - - -
267A ILE* 3.6 11.7 - - - +
283A ILE* 5.2 4.0 - - + -
284A VAL* 1.3 74.9 - - - +
286A SER* 1.3 65.4 + - - +
289A ILE* 3.5 18.3 - - + +
290A GLU* 4.3 13.0 - - + +
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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