Contacts of the helix formed by residues 93 - 101 (chain A) in PDB entry 1DLS
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 6.2 0.4 - - + -
51A ILE* 3.8 36.8 - - + -
75A LEU* 4.1 12.7 - - + +
92A SER* 1.3 71.7 - - - +
94A ASP* 1.3 57.3 - - - +
96A ALA* 3.1 4.3 + - - +
97A LEU* 2.9 54.6 + - + +
114A ILE* 4.2 14.1 - - + -
120A VAL* 5.0 5.6 - - + +
123A GLU* 3.6 40.5 + - + +
124A ALA* 4.1 21.1 - - + +
127A HIS* 4.6 9.2 - - + -
187A NDP 4.5 7.7 + - - +
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Residues in contact with ASP 94 (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 SER* 3.2 6.6 + - - +
93A LEU* 1.3 78.0 - - - +
95A ASP* 1.3 52.6 + - - +
97A LEU* 3.2 7.3 + - - +
98A LYS* 2.7 60.8 + - - +
123A GLU* 4.4 12.2 + - - +
127A HIS* 3.7 27.8 + - - -
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Residues in contact with ASP 95 (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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90A SER* 4.1 13.7 + - - +
91A ARG* 4.5 11.5 + - - +
92A SER* 3.2 24.5 + - - +
94A ASP* 1.3 74.6 - - - +
96A ALA* 1.4 69.0 + - - +
98A LYS* 2.6 41.4 + - - +
99A LEU* 3.0 24.4 + - - +
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Residues in contact with ALA 96 (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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49A LEU* 4.9 2.3 - - - +
51A ILE* 3.9 18.8 - - + -
73A LEU* 3.8 32.0 - - + +
75A LEU* 4.1 4.9 - - + -
90A SER* 3.5 11.2 + - - +
92A SER 3.0 13.2 + - - +
93A LEU* 3.1 10.1 + - - +
95A ASP* 1.4 79.8 - - - +
97A LEU* 1.3 65.3 + - - +
99A LEU* 3.3 16.5 - - - +
100A THR* 3.6 9.0 + - - -
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Residues in contact with LEU 97 (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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4A LEU* 4.5 15.0 - - + -
51A ILE* 4.1 22.0 - - + -
93A LEU* 2.9 35.7 + - + +
94A ASP* 3.8 8.3 - - - +
96A ALA* 1.3 74.3 - - - +
98A LYS* 1.3 65.0 + - - +
99A LEU 3.0 2.8 + - - -
100A THR* 3.2 25.0 + - - +
101A GLU* 4.0 2.8 + - - +
112A VAL* 4.4 16.6 - - + -
127A HIS* 3.7 34.1 - - + +
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Residues in contact with LYS 98 (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 SER* 4.8 0.2 + - - -
94A ASP* 2.7 49.3 + - - +
95A ASP* 2.6 31.0 + - - +
97A LEU* 1.3 69.9 - - - +
99A LEU* 1.3 57.6 + - - +
101A GLU* 2.7 46.9 - - - +
102A GLN* 2.8 12.1 + - - +
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Residues in contact with LEU 99 (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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49A LEU* 5.5 1.1 - - + -
73A LEU* 4.3 13.9 - - + -
88A PHE* 3.9 26.5 - - + -
89A LEU 5.6 2.2 - - - +
90A SER* 4.6 13.0 - - - +
95A ASP 3.0 12.2 + - - +
96A ALA 3.3 14.1 - - - +
97A LEU 3.0 0.6 - - - -
98A LYS* 1.3 72.1 - - - +
100A THR* 1.3 59.9 + - - +
101A GLU 3.0 5.8 - - - -
102A GLN* 3.2 32.1 + - + +
104A GLU* 5.0 6.7 - - - +
105A LEU* 3.0 45.4 - - + +
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Residues in contact with THR 100 (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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1A VAL* 2.8 41.0 - - + +
49A LEU* 3.8 19.4 - - - +
96A ALA 3.6 12.0 + - - -
97A LEU* 3.2 16.9 + - - +
99A LEU* 1.3 78.0 - - - +
101A GLU* 1.3 57.8 + - - +
102A GLN 3.4 0.4 - - - -
105A LEU* 3.7 11.4 - - - +
106A ALA* 3.0 26.9 + - - +
109A VAL* 4.5 15.3 - - + +
112A VAL* 4.7 7.1 - - + +
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Residues in contact with GLU 101 (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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1A VAL* 5.8 5.6 - - + -
97A LEU 4.7 2.5 - - - +
98A LYS* 2.7 40.5 + - - +
99A LEU 3.0 0.6 - - - -
100A THR* 1.3 80.3 - - + +
102A GLN* 1.3 72.8 + - - +
103A PRO* 3.7 4.5 - - - +
106A ALA* 4.1 8.1 - - - +
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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