Contacts of the strand formed by residues 104 - 109 (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 ARG 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU 4.0 0.2 - - - -
103A ASP* 1.3 82.3 - - - +
105A ALA* 1.3 59.3 + - - +
283A ILE* 3.7 0.9 - - - +
284A VAL* 3.2 4.4 - - - +
285A THR* 2.8 46.9 + - + +
287A ALA* 3.3 35.2 + - - +
290A GLU* 2.8 47.5 + - + +
291A GLU* 2.8 32.7 + - - +
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Residues in contact with ALA 105 (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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91A ALA* 4.2 34.6 + - + +
94A LEU* 4.2 23.3 - - + -
103A ASP 4.3 0.8 + - - -
104A ARG* 1.3 74.8 - - - +
106A LEU* 1.3 61.6 + - - +
107A LEU* 4.4 6.0 + - + +
282A ALA* 5.3 0.2 - - + -
283A ILE* 3.1 10.5 - - - +
284A VAL* 4.4 7.2 - - + -
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Residues in contact with LEU 106 (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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105A ALA* 1.3 74.7 - - - +
107A LEU* 1.3 61.2 + - - +
108A LEU* 3.7 30.9 + - + +
117A ALA* 4.0 17.0 - - + -
121A MET* 5.7 1.3 - - + -
282A ALA* 3.0 26.3 - - - +
283A ILE* 3.0 24.6 + - + +
298A TYR* 4.2 16.8 - - + +
300A PHE* 4.4 13.9 - - + +
305A VAL* 3.9 23.3 - - + -
306A SER* 5.6 1.3 - - - +
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Residues in contact with LEU 107 (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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87A VAL* 3.7 46.2 - - + +
90A LEU* 4.1 33.2 - - + -
91A ALA* 4.6 5.2 - - + +
94A LEU* 4.3 8.3 - - + -
105A ALA* 4.5 9.0 - - + +
106A LEU* 1.3 82.5 - - - +
108A LEU* 1.3 59.6 + - - +
274A LEU* 5.6 0.2 - - + -
280A LEU* 4.6 8.3 - - + -
281A ALA 3.6 3.6 - - - +
282A ALA* 3.9 15.7 - - + -
304A HIS 4.1 0.6 - - - +
305A VAL* 3.3 8.9 - - - +
306A SER* 3.0 32.8 + - - +
307A ASP 5.7 0.2 - - - +
311A ALA* 4.3 7.4 - - + -
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Residues in contact with LEU 108 (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 LEU* 3.7 19.0 + - + +
107A LEU* 1.3 78.3 - - - +
109A SER* 1.3 67.6 + - - +
110A THR 4.6 0.7 - - - +
113A GLU* 3.4 20.9 - - + +
114A SER* 4.0 12.6 - - - -
117A ALA* 3.9 27.1 - - + -
279A PRO 4.2 1.2 - - - +
280A LEU* 3.5 12.1 - - - +
281A ALA* 2.9 31.8 + - + +
282A ALA* 5.1 0.4 - - - -
283A ILE* 4.7 3.1 - - + -
300A PHE* 3.9 9.9 - - + -
302A THR* 3.6 32.5 - - + +
304A HIS 4.8 4.1 - - - +
305A VAL* 4.0 17.3 - - + +
310A PRO* 5.5 0.9 - - - +
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Residues in contact with SER 109 (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 LEU* 1.3 77.8 + - - +
110A THR* 1.3 68.8 + - - +
113A GLU* 2.6 22.6 + - - -
279A PRO* 3.3 39.0 + - - +
280A LEU 3.3 4.7 + - - +
281A ALA* 3.9 4.0 - - - -
302A THR* 5.1 0.5 + - - -
304A HIS* 3.6 33.0 + - - +
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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