Contacts of the helix formed by residues 99 - 108 (chain A) in PDB entry 2GDZ
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 ASN 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ASN* 2.9 33.3 + - - +
98A LYS* 1.3 81.6 + - - +
100A TRP* 1.3 62.2 + - - +
101A GLU* 3.3 9.2 - - - -
102A LYS* 3.3 25.3 + - + +
103A THR* 3.4 13.5 + - - -
198A GLU 4.5 4.3 - - - +
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Residues in contact with TRP 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 ASN 3.4 11.0 - - - +
97A GLU 3.7 18.6 - - - +
98A LYS 3.2 15.3 + - - -
99A ASN* 1.3 74.3 - - - +
101A GLU* 1.3 101.5 + - + +
103A THR* 3.3 3.8 + - - -
104A LEU* 3.0 42.8 + - + +
150A VAL* 3.6 36.4 - - + +
202A GLN* 6.3 1.1 - - - -
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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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98A LYS 4.4 1.6 - - - +
99A ASN* 4.0 5.9 - - - -
100A TRP* 1.3 131.5 + - + +
102A LYS* 1.3 55.7 + - - +
104A LEU* 3.2 8.9 + - - +
105A GLN* 3.0 32.0 + - + +
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Residues in contact with LYS 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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37A TRP* 3.7 36.8 - - - -
64A ASP* 5.9 0.4 - - - -
94A VAL* 5.2 1.3 - - + -
99A ASN* 3.3 20.7 + - + +
101A GLU* 1.3 75.7 - - - +
103A THR* 1.3 58.6 + - - +
105A GLN* 3.1 10.4 + - + +
106A ILE* 2.8 42.6 + - + +
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Residues in contact with THR 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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94A VAL* 3.8 21.8 - - - +
96A ASN* 2.6 46.8 + - - +
99A ASN 3.4 1.8 + - - -
100A TRP* 3.3 10.3 + - - +
102A LYS* 1.3 78.9 - - - +
104A LEU* 1.3 57.7 + - - +
107A ASN* 2.8 57.1 + - + +
150A VAL* 4.6 11.7 - - + +
151A TYR* 4.6 12.3 - - + +
154A SER* 4.9 0.9 - - - +
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Residues in contact with LEU 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 TRP* 3.0 38.6 + - + +
101A GLU* 3.2 8.9 + - - +
103A THR* 1.3 76.5 - - - +
105A GLN* 1.3 63.8 + - + +
108A LEU* 3.0 23.6 + - + +
109A VAL* 3.0 26.3 + - + +
150A VAL* 3.6 20.4 - - + +
153A ALA* 4.6 6.3 - - + -
154A SER* 3.9 33.0 - - - +
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Residues in contact with GLN 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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66A ALA* 4.4 22.6 - - + +
101A GLU* 3.0 20.3 + - + +
102A LYS* 3.4 13.5 - - + +
104A LEU* 1.3 75.8 - - + +
106A ILE* 1.3 59.3 + - + +
109A VAL* 3.4 31.7 - - - +
110A SER* 2.9 35.0 + - - -
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Residues in contact with ILE 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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37A TRP* 3.9 17.3 - - + -
65A VAL* 4.2 7.0 - - + +
66A ALA* 4.2 10.8 - - + -
92A ALA 4.4 7.5 - - - +
93A GLY* 4.1 10.8 - - - -
94A VAL* 4.1 20.6 - - + -
102A LYS* 2.8 38.5 + - + +
103A THR 4.1 0.7 - - - +
105A GLN* 1.3 78.8 - - - +
107A ASN* 1.3 75.0 + - - +
110A SER* 3.2 24.7 - - - -
111A VAL* 4.2 2.8 + - - +
300A NAD 3.6 43.1 - - + +
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Residues in contact with ASN 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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92A ALA 4.7 5.2 - - - -
93A GLY* 3.1 8.0 - - - -
94A VAL* 2.8 47.7 + - - +
103A THR* 2.8 30.2 + - - +
106A ILE* 1.3 74.1 - - - +
108A LEU* 1.3 55.9 + - - +
111A VAL* 3.1 21.5 - - - +
151A TYR* 3.5 17.2 - - - -
154A SER* 3.2 28.3 + - - +
155A LYS* 4.2 10.0 + - - +
158A ILE* 3.2 14.0 - - + +
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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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104A LEU* 3.0 20.8 + - + +
106A ILE 3.4 0.2 - - - -
107A ASN* 1.3 78.8 - - - +
109A VAL* 1.3 71.9 + - + +
110A SER 3.2 1.6 - - - -
111A VAL* 3.1 4.1 + - + +
112A ILE* 3.1 47.8 + - + +
153A ALA 4.9 1.6 - - - +
154A SER* 3.9 21.8 - - - +
157A GLY* 3.6 40.2 - - - +
158A ILE* 3.7 10.5 - - + +
161A PHE* 5.2 0.4 - - + -
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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