Contacts of the helix formed by residues 94 - 104 (chain A) in PDB entry 1D8L
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 SER 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A THR* 5.4 5.6 - - - +
90A LEU* 5.1 2.7 - - - +
93A MET* 1.3 80.4 - - - +
95A ALA* 1.3 63.5 + - - +
96A GLN* 3.2 9.8 + - - +
97A GLN* 2.5 41.1 + - - +
98A PHE* 3.4 16.5 + - - +
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Residues in contact with ALA 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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67A GLN* 5.8 2.0 - - + -
68A GLU* 4.9 20.6 - - + +
71A LEU* 4.3 17.3 - - + +
90A LEU* 5.1 3.1 - - + +
94A SER* 1.3 76.0 - - - +
96A GLN* 1.3 61.4 - - - +
98A PHE* 3.6 3.1 + - - +
99A VAL* 3.2 28.8 + - - +
139A LEU* 3.4 23.5 - - + +
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Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER* 3.2 6.9 + - - +
95A ALA* 1.3 78.2 - - - +
97A GLN* 1.3 64.4 + - - +
99A VAL* 3.4 16.1 + - - +
100A ASN* 3.0 48.0 + - - +
138A ASP 4.7 0.3 - - - +
139A LEU* 2.8 46.0 + - - +
140A PHE* 5.2 0.4 - - - +
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Residues in contact with GLN 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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92A GLY 4.6 2.6 + - - -
93A MET* 3.5 24.2 - - + +
94A SER* 2.5 46.1 + - - +
96A GLN* 1.3 75.6 - - - +
98A PHE* 1.3 53.1 + - - +
100A ASN* 3.1 9.6 + - - +
101A ALA* 2.8 37.6 + - - +
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Residues in contact with PHE 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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71A LEU* 3.6 42.6 - - + -
75A LEU* 3.5 23.6 - - + -
89A ILE* 3.7 30.7 - - + -
90A LEU* 5.3 1.3 - - + -
93A MET* 3.8 14.3 - - + -
94A SER 3.4 14.6 + - - +
95A ALA 3.8 3.4 - - - +
96A GLN 3.3 0.2 - - - -
97A GLN* 1.3 79.2 - - - +
99A VAL* 1.3 57.9 + - - +
101A ALA* 3.8 2.2 - - - +
102A VAL* 2.9 57.3 + - + +
110A LEU* 4.2 24.9 - - + -
124A LEU* 4.7 3.1 - - + -
128A MET* 3.9 13.7 - - + -
132A PHE* 4.0 9.0 - + - -
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Residues in contact with VAL 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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71A LEU* 4.8 3.4 - - + -
95A ALA 3.2 19.2 + - - +
96A GLN* 3.8 12.1 - - - +
97A GLN 3.3 0.8 - - - -
98A PHE* 1.3 75.2 - - + +
100A ASN* 1.3 63.8 + - - +
102A VAL* 3.3 1.2 + - - +
103A GLU* 3.0 38.2 + - + +
132A PHE* 3.4 39.9 - - + -
139A LEU* 3.4 21.5 - - + -
140A PHE 4.0 19.5 - - - +
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Residues in contact with ASN 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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96A GLN* 3.0 43.9 + - - +
97A GLN* 3.5 6.4 - - - +
99A VAL* 1.3 80.6 - - - +
101A ALA* 1.3 58.1 + - - +
103A GLU* 3.5 9.3 + - - +
104A ARG* 3.0 38.2 + - - +
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Residues in contact with ALA 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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93A MET* 5.2 1.8 - - - -
97A GLN 2.8 21.7 + - - +
98A PHE* 3.8 6.5 - - - +
100A ASN* 1.3 74.6 - - - +
102A VAL* 1.3 59.8 + - - +
104A ARG* 3.6 10.3 + - - +
105A GLU 3.5 2.1 + - - -
106A GLU* 2.9 42.7 + - + +
109A ALA* 4.0 26.9 - - + -
110A LEU* 5.0 7.9 - - + -
125A ILE* 5.6 0.4 - - - -
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Residues in contact with VAL 102 (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 PHE* 2.9 51.7 + - + +
99A VAL 3.8 2.7 - - - +
101A ALA* 1.3 75.7 - - + +
103A GLU* 1.3 64.6 + - - +
105A GLU* 3.1 14.4 + - - -
110A LEU* 5.2 3.8 - - + -
124A LEU 5.6 0.2 - - - -
125A ILE* 3.8 33.5 - - + +
128A MET* 3.8 11.0 - - + -
129A LYS* 3.7 37.6 + - + +
132A PHE* 4.3 11.4 - - + -
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Residues in contact with GLU 103 (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* 3.0 29.8 + - + +
100A ASN* 3.9 6.7 - - - +
101A ALA 3.4 0.2 - - - -
102A VAL* 1.3 78.2 - - - +
104A ARG* 1.3 55.8 + - + +
105A GLU* 3.4 10.4 - - - +
129A LYS* 3.7 20.7 + - - +
132A PHE* 3.7 26.0 - - + +
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Residues in contact with ARG 104 (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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100A ASN* 3.0 31.1 + - - +
101A ALA* 3.8 13.1 - - - +
102A VAL 3.2 0.2 - - - -
103A GLU* 1.3 74.5 - - + +
105A GLU* 1.3 72.2 + - - +
106A GLU* 3.0 41.6 + - + +
109A ALA* 5.8 2.4 - - - +
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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