Contacts of the helix formed by residues 95 - 111 (chain A) in PDB entry 2Z3Q
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ALA 4.2 7.4 - - - +
24A THR* 4.7 6.2 - - + +
94A LYS* 1.3 79.2 - - - +
96A ILE* 1.3 60.0 + - - +
97A LYS* 3.1 12.2 + - - +
98A GLU* 2.9 40.1 + - - +
99A PHE* 2.9 23.7 + - - +
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Residues in contact with ILE 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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16A ILE* 3.7 28.9 - - + -
21A ILE* 3.7 34.5 - - + +
22A ASP* 5.0 0.2 - - - -
23A ALA* 3.4 25.5 + - + +
25A LEU* 3.4 28.5 - - + -
50A ILE* 3.9 31.2 - - + -
95A ASN* 1.3 73.1 - - - +
97A LYS* 1.3 64.3 + - - +
99A PHE* 3.5 3.7 - - - +
100A LEU* 3.0 28.6 + - + +
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Residues in contact with LYS 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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13A GLU* 5.5 12.8 + - - +
16A ILE* 5.5 1.4 - - - +
95A ASN* 3.1 11.7 + - - +
96A ILE* 1.3 76.9 - - - +
98A GLU* 1.3 67.8 + - + +
100A LEU* 4.0 5.3 - - - +
101A GLN* 3.1 25.7 + - + +
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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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27A THR* 4.1 2.1 - - - +
29A SER* 4.9 0.4 + - - +
94A LYS* 3.6 27.7 + - + +
95A ASN* 2.9 48.8 + - - +
97A LYS* 1.3 75.9 - - + +
99A PHE* 1.3 64.9 + - - +
101A GLN* 3.5 5.9 + - - +
102A SER* 3.1 27.4 + - - -
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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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25A LEU* 3.6 29.6 - - + -
26A TYR 3.5 12.6 - - - -
27A THR* 3.3 30.2 + - - +
43A PHE* 3.4 51.9 - + - -
46A GLU* 3.7 21.5 - - + -
47A LEU* 3.8 7.9 - - + -
50A ILE* 4.0 14.6 - - + -
94A LYS 4.8 0.2 - - - +
95A ASN 2.9 16.7 + - - +
96A ILE* 3.2 7.6 + - - +
98A GLU* 1.3 76.0 - - - +
100A LEU* 1.3 68.7 + - + +
102A SER 3.3 2.1 + - - -
103A PHE* 2.8 42.1 + + - +
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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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9A LEU* 4.0 29.0 - - + +
12A ILE* 4.3 13.7 - - + -
13A GLU* 4.0 32.3 - - + +
16A ILE* 3.9 26.5 - - + -
47A LEU* 4.4 2.2 - - + -
50A ILE* 4.3 11.0 - - + -
96A ILE* 3.0 24.9 + - + +
97A LYS* 4.1 4.0 - - - +
99A PHE* 1.3 91.7 - - + +
101A GLN* 1.3 64.6 + - - +
103A PHE* 3.2 4.8 + - + +
104A VAL* 3.0 29.2 + - + +
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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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97A LYS* 3.1 21.1 + - + +
98A GLU* 3.8 7.6 - - - +
99A PHE 3.4 0.2 - - - -
100A LEU* 1.3 76.0 - - - +
102A SER* 1.3 58.3 - - - +
104A VAL* 3.3 16.1 + - - +
105A HIS* 3.1 54.3 + - + -
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Residues in contact with SER 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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27A THR* 3.6 20.2 - - - -
28A GLU 3.9 6.7 - - - +
29A SER* 2.8 29.5 + - - -
43A PHE* 3.8 11.7 - - - -
98A GLU 3.1 16.1 + - - -
99A PHE 3.7 0.9 - - - -
101A GLN* 1.3 73.7 - - - +
103A PHE* 1.3 67.1 + - - +
105A HIS* 3.3 14.5 + - - +
106A ILE* 3.1 21.8 + - - +
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Residues in contact with PHE 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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5A VAL* 4.8 2.7 - - + -
9A LEU* 3.6 21.5 - - + -
40A MET* 3.9 12.6 - - - -
43A PHE* 3.5 47.7 - + + -
44A LEU* 4.0 22.7 - - + -
47A LEU* 3.7 20.6 - - + -
66A LEU* 4.1 8.5 - - + -
99A PHE* 2.8 32.4 + + - +
100A LEU* 3.2 12.5 + - + +
102A SER* 1.3 76.3 - - - +
104A VAL* 1.3 63.4 + - - +
106A ILE* 2.9 9.9 - - + +
107A VAL* 2.9 42.1 + - + +
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Residues in contact with VAL 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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6A ILE* 4.8 15.9 - - + -
9A LEU* 3.8 28.9 - - + +
10A LYS 5.7 0.4 - - - +
100A LEU* 3.0 18.3 + - + +
101A GLN* 3.4 24.7 - - - +
103A PHE* 1.3 76.5 - - - +
105A HIS* 1.3 62.1 + - + +
107A VAL* 3.4 3.5 + - - +
108A GLN* 2.8 55.5 + - + +
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Residues in contact with HIS 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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29A SER 5.2 8.7 + - - +
101A GLN* 3.1 47.7 + - + -
102A SER* 3.5 17.7 + - - +
103A PHE 3.3 0.4 - - - -
104A VAL* 1.3 77.7 - - + +
106A ILE* 1.3 60.6 + - - +
108A GLN* 3.4 19.0 + - - +
109A MET* 3.3 23.6 + - - +
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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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31A VAL* 3.6 38.6 - - + -
36A LYS 3.8 7.2 - - - +
39A ALA* 3.6 7.6 - - + -
40A MET* 3.6 44.2 - - + +
43A PHE* 4.0 10.1 - - + -
102A SER 3.1 11.0 + - - +
103A PHE* 2.9 25.8 - - + +
105A HIS* 1.3 72.8 - - - +
107A VAL* 1.3 73.1 + - - +
108A GLN 3.0 1.3 - - - -
109A MET* 3.0 19.2 + - - +
110A PHE* 3.3 26.7 + - + -
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Residues in contact with VAL 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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2A TRP* 3.2 39.7 - - + +
5A VAL* 3.6 25.1 - - + -
6A ILE* 3.4 20.9 - - + -
9A LEU* 4.2 3.4 - - + -
40A MET* 4.1 13.5 - - + -
103A PHE* 2.9 33.4 + - + +
104A VAL* 3.9 4.5 - - - +
106A ILE* 1.3 80.9 - - - +
108A GLN* 1.3 63.1 + - - +
110A PHE* 3.0 16.0 + - - +
111A ILE* 3.2 10.9 + - - +
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Residues in contact with GLN 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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6A ILE* 3.8 23.3 - - + +
104A VAL* 2.8 41.6 + - - +
105A HIS* 3.6 18.7 - - - +
106A ILE 3.0 0.4 - - - -
107A VAL* 1.3 77.4 - - - +
109A MET* 1.3 61.3 + - - +
111A ILE* 3.0 28.9 + - + +
112A ASN* 3.7 3.6 + - - -
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Residues in contact with MET 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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31A VAL* 4.1 35.0 - - + +
33A PRO* 4.1 25.6 - - + -
36A LYS* 3.8 27.8 - - + -
105A HIS 3.3 14.2 + - - +
106A ILE* 3.0 13.9 + - + +
108A GLN* 1.3 76.9 - - - +
110A PHE* 1.3 62.7 + - + +
111A ILE 3.5 5.5 - - - +
112A ASN* 3.7 5.5 + - - +
114A SER* 3.2 21.3 + - - -
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Residues in contact with PHE 110 (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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2A TRP* 3.6 39.4 - + + -
36A LYS* 3.4 63.5 - - + -
37A VAL* 4.1 9.4 - - + -
40A MET* 3.6 25.1 - - + -
73A SER 5.6 1.3 - - - -
74A LEU* 3.7 21.1 - - + -
106A ILE* 3.3 22.6 + - + -
107A VAL 3.0 10.1 + - - +
109A MET* 1.3 74.4 - - - +
111A ILE* 1.3 62.6 + - - +
112A ASN 3.3 1.2 + - - -
113A THR* 3.0 13.0 + - - -
114A SER* 2.8 35.2 + - - +
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Residues in contact with ILE 111 (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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0A SER* 4.2 15.5 - - - +
2A TRP* 3.6 21.1 - - + -
3A VAL* 3.9 25.8 - - + +
6A ILE* 3.4 32.5 - - + -
107A VAL 3.2 8.5 + - - +
108A GLN* 3.0 14.3 + - + +
109A MET 3.5 0.2 - - - +
110A PHE* 1.3 74.0 - - - +
112A ASN* 1.3 83.7 + - - +
113A THR* 3.8 4.5 - - - -
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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