Contacts of the helix formed by residues 41 - 54 (chain A) in PDB entry 3ZYQ
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 GLN 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLY* 3.7 20.1 - - - +
39A ASP 5.3 0.3 - - - -
40A THR* 1.3 78.2 - - - +
42A ALA* 1.3 60.5 - - - +
43A LYS* 3.4 6.2 + - + +
44A TYR* 3.4 13.3 + - + +
45A ALA* 2.9 26.9 + - - +
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Residues in contact with ALA 42 (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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35A ILE* 4.3 6.2 - - + +
40A THR 3.5 2.6 + - - -
41A GLN* 1.3 73.4 - - - +
43A LYS* 1.3 57.3 + - - +
45A ALA* 4.3 6.3 - - - -
46A VAL* 2.8 35.3 + - - +
78A THR* 3.3 50.3 + - + +
79A VAL* 3.9 15.3 - - + -
82A GLU* 4.1 2.5 - - + +
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Residues in contact with LYS 43 (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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41A GLN* 3.3 4.7 - - + +
42A ALA* 1.3 78.2 - - - +
44A TYR* 1.3 58.3 + - - +
46A VAL* 3.9 0.5 - - - +
47A ASN* 2.8 51.1 + - - +
82A GLU* 2.8 53.1 + - - +
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Residues in contact with TYR 44 (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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8A PHE* 3.8 21.1 - + + -
9A GLU* 2.6 38.8 + - - +
40A THR* 4.3 10.5 - - + -
41A GLN* 3.4 17.4 + - + +
42A ALA 3.4 0.2 - - - -
43A LYS* 1.3 79.0 - - - +
45A ALA* 1.3 58.8 + - - +
47A ASN* 3.8 7.3 - - + +
48A SER* 2.8 46.0 + - - -
51A LYS* 5.5 5.2 - - - -
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Residues in contact with ALA 45 (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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8A PHE* 3.5 25.7 - - + -
35A ILE* 3.6 31.4 - - + -
40A THR* 4.0 6.3 - - + -
41A GLN 2.9 18.2 + - - +
42A ALA 3.7 3.8 - - - +
44A TYR* 1.3 78.2 - - - +
46A VAL* 1.3 58.9 + - + +
48A SER* 3.1 4.3 + - - -
49A ILE* 3.0 34.1 + - + +
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Residues in contact with VAL 46 (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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35A ILE* 5.7 0.2 - - + -
42A ALA 2.8 26.1 + - - +
43A LYS 4.2 1.3 - - - +
45A ALA* 1.3 71.4 - - + +
47A ASN* 1.3 62.1 + - - +
49A ILE* 3.3 7.4 + - + +
50A LYS* 2.8 52.4 + - + +
68A MET* 4.3 7.9 - - + -
71A VAL* 4.8 9.9 - - + -
79A VAL* 4.1 28.7 - - + -
82A GLU* 3.9 27.4 - - + +
83A VAL* 4.0 13.0 - - + -
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Residues in contact with ASN 47 (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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43A LYS* 2.8 38.9 + - - +
44A TYR* 3.8 7.6 - - + +
46A VAL* 1.3 77.1 - - - +
48A SER* 1.3 61.3 + - - +
50A LYS* 3.4 21.8 + - - +
51A LYS* 3.2 34.8 + - - +
82A GLU* 4.8 4.0 - - - +
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Residues in contact with SER 48 (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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8A PHE* 3.6 23.3 - - - -
9A GLU* 5.7 1.0 - - - +
12A LEU* 3.7 17.0 - - - +
44A TYR* 2.8 40.6 + - - -
45A ALA 3.1 5.1 + - - -
47A ASN* 1.3 75.4 - - - +
49A ILE* 1.3 62.3 + - - +
51A LYS* 3.4 34.2 + - - +
52A LYS* 3.6 6.8 + - - +
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Residues in contact with ILE 49 (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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8A PHE* 4.6 7.9 - - + -
12A LEU* 3.9 26.2 - - + -
31A ILE* 5.1 0.2 - - + -
45A ALA* 3.0 22.8 + - + +
46A VAL* 3.7 9.4 - - + +
48A SER* 1.3 73.5 - - - +
50A LYS* 1.3 65.3 + - - +
52A LYS* 3.1 6.5 + - - +
53A VAL* 3.0 21.9 + - + +
64A ALA* 3.5 26.5 - - + +
67A VAL* 3.8 19.1 - - + -
68A MET* 4.0 21.3 - - + +
71A VAL* 4.0 27.4 - - + -
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Residues in contact with LYS 50 (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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46A VAL* 2.8 35.3 + - + +
47A ASN* 3.7 20.3 + - - +
48A SER 3.3 0.2 - - - -
49A ILE* 1.3 76.9 - - - +
51A LYS* 1.3 61.9 + - - +
53A VAL* 3.2 10.3 + - + +
54A ASN* 2.9 35.7 + - - +
68A MET* 3.6 16.8 - - + -
82A GLU* 3.2 13.8 + - - +
83A VAL* 5.2 0.2 - - - -
85A ASN* 5.1 0.6 - - - +
87A GLN* 5.9 2.2 - - - +
88A THR* 2.8 43.0 + - + +
91A GLU* 4.0 17.4 + - - +
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Residues in contact with LYS 51 (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 TYR* 5.5 4.6 - - - -
47A ASN* 3.2 16.1 + - - +
48A SER* 3.5 36.3 + - - +
49A ILE 3.2 0.4 - - - -
50A LYS* 1.3 78.1 - - - +
52A LYS* 1.3 61.6 + - + +
54A ASN* 3.6 14.2 + - - +
55A ASP* 3.8 14.2 + - - +
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Residues in contact with LYS 52 (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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12A LEU* 4.2 20.0 - - + -
13A ASP* 3.3 27.9 + - - +
16A THR* 3.8 27.0 + - + +
48A SER 3.8 12.6 - - - +
49A ILE* 3.1 9.7 + - - +
51A LYS* 1.3 75.2 - - + +
53A VAL* 1.3 64.2 + - - +
54A ASN 3.2 2.0 - - - -
55A ASP* 3.0 25.7 + - - +
60A VAL* 4.0 16.4 - - + +
61A ALA* 3.7 9.9 - - - -
64A ALA* 3.4 16.9 - - + +
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Residues in contact with VAL 53 (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 ILE* 3.0 24.8 + - + +
50A LYS* 3.2 12.5 + - + +
52A LYS* 1.3 75.0 - - - +
54A ASN* 1.3 59.9 + - - +
55A ASP 3.2 1.1 + - - +
61A ALA* 3.3 23.4 - - - +
64A ALA* 3.7 20.6 - - + +
65A LEU* 3.8 36.3 - - + +
68A MET* 4.6 8.3 - - + -
92A LEU* 4.8 6.1 - - + -
95A LEU* 3.5 33.0 - - + +
99A GLN* 5.6 0.3 + - - -
104A VAL* 5.5 0.2 - - - +
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Residues in contact with ASN 54 (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 LYS* 2.9 28.1 + - - +
51A LYS* 3.9 10.1 - - - +
52A LYS 3.2 1.2 - - - -
53A VAL* 1.3 76.9 - - - +
55A ASP* 1.3 63.9 + - - +
56A LYS 3.7 1.6 + - - -
91A GLU* 5.1 12.5 + - - +
95A LEU* 3.8 20.4 - - - +
98A ARG* 3.4 25.3 + - - +
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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