Contacts of the helix formed by residues 91 - 101 (chain A) in PDB entry 3GZN
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ASP 2.9 25.6 + - - -
69A GLY* 4.3 3.0 - - - -
70A ASN 3.3 15.7 + - - +
71A GLN* 4.6 2.0 - - - +
89A GLY 4.1 0.4 + - - -
90A LYS* 1.3 74.7 - - - +
92A ARG* 1.3 65.3 + - - +
93A ALA* 3.4 6.5 + - - +
94A GLU* 2.9 39.1 + - + +
95A ALA* 3.1 28.4 + - - +
111A PHE* 3.9 0.9 - - - -
113A GLU* 3.7 35.6 + - - +
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Residues in contact with ARG 92 (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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44A ASN* 3.9 12.3 + - - +
45A ALA* 3.4 28.7 - - - +
46A THR* 4.1 10.5 - - - +
68A ASP* 2.7 42.6 + - - +
70A ASN* 2.8 48.9 + - - +
71A GLN 4.5 1.2 + - - -
72A VAL* 3.9 22.7 - - + +
76A ASP* 3.0 30.5 + - - +
83A LEU* 4.1 10.4 - - + +
90A LYS 3.5 0.6 + - - -
91A ASN* 1.3 70.6 - - - +
93A ALA* 1.3 65.9 + - - +
95A ALA* 4.0 0.7 - - - +
96A ALA* 3.0 27.4 + - - +
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Residues in contact with ALA 93 (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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45A ALA* 4.5 0.2 - - - -
66A ILE* 3.2 41.6 - - + +
68A ASP* 3.5 25.8 - - + +
91A ASN* 3.4 10.9 + - - +
92A ARG* 1.3 78.2 - - - +
94A GLU* 1.3 62.8 + - - +
96A ALA* 3.8 1.9 - - - +
97A MET* 3.1 24.9 + - - +
111A PHE* 3.8 9.0 - - + +
112A VAL 4.2 2.5 - - - +
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Residues in contact with GLU 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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90A LYS* 5.6 7.0 - - + +
91A ASN* 2.9 29.7 + - + +
93A ALA* 1.3 74.2 - - - +
95A ALA* 1.3 66.1 + - - +
97A MET* 3.5 3.2 + - - +
98A GLU* 3.2 40.8 + - + +
111A PHE* 3.3 44.4 - - + -
113A GLU* 5.5 2.8 - - - +
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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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72A VAL* 4.3 2.0 - - + -
82A PHE 4.2 2.2 - - - -
83A LEU* 3.9 17.3 - - + -
87A SER* 3.9 23.8 - - - +
90A LYS* 5.1 7.4 - - + +
91A ASN 3.1 19.9 + - - +
92A ARG 4.0 0.4 - - - +
94A GLU* 1.3 77.2 - - - +
96A ALA* 1.3 62.1 + - - +
98A GLU* 3.3 23.1 + - - +
99A PHE* 3.3 19.7 + - + -
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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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45A ALA* 3.7 22.4 - - + -
50A THR* 4.0 15.0 - - + -
66A ILE* 3.9 7.0 - - + -
82A PHE* 3.5 12.8 - - - +
83A LEU* 3.8 6.5 - - + +
92A ARG 3.0 19.4 + - - +
93A ALA 3.8 2.5 - - - +
95A ALA* 1.3 76.8 - - - +
97A MET* 1.3 57.4 + - - +
99A PHE* 3.3 4.3 + - - +
100A LEU* 3.0 33.7 + - - +
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Residues in contact with MET 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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64A PHE* 4.1 14.1 - - + -
66A ILE* 4.1 8.9 - - + +
93A ALA 3.1 18.2 + - - +
94A GLU* 3.8 3.8 - - - +
95A ALA 3.2 0.4 - - - -
96A ALA* 1.3 74.9 - - - +
98A GLU* 1.3 69.1 + - - +
100A LEU* 4.0 4.4 - - - +
101A GLN* 3.0 47.8 + - - +
109A GLY 3.4 24.2 - - - +
110A SER* 3.6 20.0 - - - +
111A PHE* 3.4 31.9 - - + -
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Residues in contact with GLU 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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90A LYS* 5.9 3.5 - - - +
94A GLU* 3.2 32.4 + - + +
95A ALA* 3.3 16.0 + - - +
97A MET* 1.3 83.4 - - + +
99A PHE* 1.3 69.2 + - + +
101A GLN* 4.0 7.1 + - - +
102A GLU* 3.3 26.4 + - - +
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Residues in contact with PHE 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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82A PHE* 3.1 49.7 - - + +
83A LEU* 4.2 0.2 - - - -
84A GLN* 3.0 43.3 - - + -
86A SER* 5.1 3.1 - - - -
87A SER* 4.0 16.6 - - - -
95A ALA* 3.3 17.6 + - + -
96A ALA 3.3 1.4 + - - +
97A MET 3.1 0.4 - - - -
98A GLU* 1.3 81.0 - - + +
100A LEU* 1.3 64.9 + - - +
101A GLN 3.2 1.8 - - - -
102A GLU* 3.2 34.4 + - - +
103A LEU* 3.9 4.7 + - - +
135B ARG* 3.8 28.3 + - - +
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Residues in contact with LEU 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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50A THR* 3.8 31.2 - - + +
53A LEU* 3.8 30.5 - - + +
54A LYS* 3.9 16.8 - - - +
57A VAL* 3.5 15.4 - - + +
64A PHE* 4.2 12.1 - - + -
66A ILE* 4.0 12.3 - - + -
82A PHE* 3.7 31.6 - - + -
96A ALA 3.0 22.2 + - - +
97A MET 3.3 2.9 + - - +
99A PHE* 1.3 77.1 - - - +
101A GLN* 1.3 61.0 + - - +
103A LEU* 3.3 24.2 + - + +
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Residues in contact with GLN 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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57A VAL* 5.3 0.2 - - - -
64A PHE* 4.6 7.1 - - + -
97A MET* 3.0 40.6 + - - +
98A GLU* 4.1 6.5 - - - +
99A PHE 3.2 0.2 - - - -
100A LEU* 1.3 73.9 - - - +
102A GLU* 1.3 62.2 + - + +
103A LEU 3.1 6.2 + - - -
104A ASN 3.3 20.7 + - - +
105A SER* 4.1 4.8 + - - -
107A VAL* 3.6 17.9 + - - +
108A SER* 3.8 2.0 - - - +
109A GLY* 2.8 36.8 + - - +
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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