Contacts of the helix formed by residues 44 - 58 (chain A) in PDB entry 4N1T
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 THR 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A VAL* 4.1 1.6 - - - +
42A GLY 4.3 0.8 + - - -
43A GLU* 1.3 79.1 - - - +
45A ILE* 1.3 60.3 + - - +
46A GLU* 3.6 6.7 + - - +
47A ASP* 3.0 36.8 + - - +
48A GLY* 2.8 25.6 + - - -
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Residues in contact with ILE 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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6A LEU* 3.9 28.0 - - + -
8A THR* 3.4 17.0 - - + +
39A VAL* 4.2 13.7 - - + -
43A GLU 3.9 0.2 + - - -
44A THR* 1.3 74.3 - - - +
46A GLU* 1.3 59.5 + - - +
48A GLY 3.1 1.9 + - - -
49A ALA* 2.9 23.9 + - - +
84A HIS* 3.6 58.6 - - + +
86A PHE* 4.0 9.0 - - + -
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.2 6.7 + - - +
45A ILE* 1.3 80.1 - - - +
47A ASP* 1.3 63.2 + - - +
49A ALA* 3.2 2.7 + - - +
50A ARG* 3.0 38.3 + - - +
64A LEU* 3.8 42.0 + - + +
66A LYS* 4.7 12.2 - - - +
86A PHE* 3.9 24.8 - - + -
202A SO4 5.0 1.9 + - - -
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Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 3.7 14.4 - - + +
44A THR* 3.0 32.8 + - - +
46A GLU* 1.3 77.6 - - - +
48A GLY* 1.3 64.0 + - - +
50A ARG* 3.2 25.0 + - - +
51A ARG* 3.0 23.9 + - - +
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Residues in contact with GLY 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 THR* 4.0 8.5 - - - -
39A VAL* 4.9 4.0 - - - -
43A GLU* 3.3 26.5 - - - -
44A THR 2.8 13.2 + - - -
45A ILE 3.1 5.1 + - - -
47A ASP* 1.3 75.5 - - - +
49A ALA* 1.3 55.8 + - - +
51A ARG* 3.3 5.5 + - - +
52A GLU* 2.9 35.3 + - - +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 3.5 15.6 + - - -
10A VAL* 3.6 30.2 - - + +
45A ILE 2.9 7.7 + - - +
46A GLU 3.2 7.8 + - - +
48A GLY* 1.3 76.4 - - - +
50A ARG* 1.3 62.6 + - - +
52A GLU* 3.4 0.9 + - - +
53A LEU* 3.1 20.3 + - - +
64A LEU* 3.9 8.1 - - + -
86A PHE* 3.6 29.8 - - + -
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU* 3.0 34.9 + - - +
47A ASP* 3.2 29.7 + - - +
49A ALA* 1.3 76.4 - - - +
51A ARG* 1.3 58.2 + - - +
53A LEU* 3.4 2.6 + - - +
54A GLN* 3.0 63.2 + - - +
61A VAL* 3.6 28.1 + - + +
62A ASP 3.8 15.6 + - - -
64A LEU* 3.8 15.7 - - + +
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Residues in contact with ARG 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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38A LYS 3.0 24.4 + - - -
40A GLN* 3.2 33.2 - - - +
43A GLU* 2.7 41.4 + - - +
47A ASP 3.0 15.9 + - - +
48A GLY* 3.5 7.3 - - - +
50A ARG* 1.3 74.0 - - - +
52A GLU* 1.3 81.3 + - - +
54A GLN* 3.3 9.1 + - - +
55A GLU* 2.9 66.0 + - + +
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Residues in contact with GLU 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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8A THR* 3.5 10.3 - - - +
35A PHE* 4.4 2.0 - - - +
36A GLY* 3.3 16.2 - - - +
37A GLY* 3.2 38.6 - - - +
38A LYS 3.3 2.9 + - - +
48A GLY 2.9 24.0 + - - +
49A ALA 3.8 4.0 - - - +
51A ARG* 1.3 101.5 + - - +
53A LEU* 1.3 67.5 + - - +
55A GLU* 4.4 6.6 - - - +
56A GLU* 2.8 54.5 + - - +
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Residues in contact with LEU 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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10A VAL* 4.0 25.1 - - + -
12A VAL* 3.9 24.5 - - + -
35A PHE* 3.6 34.5 + - + -
49A ALA 3.1 15.0 + - - +
50A ARG* 3.7 4.5 - - - +
51A ARG 3.3 0.2 - - - -
52A GLU* 1.3 79.2 - - - +
54A GLN* 1.3 56.5 + - - +
57A SER* 2.6 56.7 + - - +
59A LEU* 4.6 7.6 - - + +
61A VAL* 3.7 31.9 - - + -
88A THR* 4.4 2.7 - - + -
91A ILE* 4.7 4.5 - - + -
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Residues in contact with GLN 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 ARG* 3.0 44.7 + - + +
51A ARG* 3.9 6.5 - - - +
52A GLU 3.2 0.2 - - - -
53A LEU* 1.3 79.2 - - + +
55A GLU* 1.3 56.6 + - + +
58A GLY* 3.1 25.9 + - - -
59A LEU 2.8 23.8 - - - +
60A THR* 3.5 16.8 - - - +
61A VAL* 3.1 26.1 + - + +
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Residues in contact with GLU 55 (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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40A GLN* 5.6 0.5 + - - -
51A ARG* 2.9 59.7 + - + +
52A GLU* 4.1 7.8 - - - +
54A GLN* 1.3 77.3 - - + +
56A GLU* 1.3 63.9 - - + +
58A GLY* 4.6 1.6 + - - -
100A GLU* 4.2 9.0 - - - +
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Residues in contact with GLU 56 (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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34A GLY 4.7 0.2 - - - +
35A PHE* 3.4 16.6 - - + -
36A GLY 2.6 45.0 + - - +
52A GLU* 2.8 30.1 + - - +
55A GLU* 1.3 81.3 - - + +
57A SER* 1.3 60.9 + - - +
96A VAL 4.3 7.4 - - - +
98A SER* 4.8 2.8 + - - -
100A GLU* 3.3 30.3 - - - +
101A MET* 3.6 36.3 - - + +
103A PRO* 4.5 0.3 - - - +
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Residues in contact with SER 57 (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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19A LEU* 4.4 4.7 - - - -
35A PHE* 3.8 28.5 - - - -
53A LEU* 2.6 30.7 + - - +
56A GLU* 1.3 78.1 - - - +
58A GLY* 1.3 58.7 + - - +
59A LEU* 3.2 25.1 + - - +
95A PRO* 3.3 9.0 - - - +
96A VAL* 2.9 29.1 + - - -
103A PRO* 4.4 5.4 - - - -
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Residues in contact with GLY 58 (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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54A GLN* 3.1 18.1 + - - -
55A GLU 4.6 1.6 + - - -
56A GLU 3.8 0.6 - - - -
57A SER* 1.3 77.4 + - - +
59A LEU* 1.3 63.9 + - - +
60A THR* 4.0 2.9 + - - -
92A GLN 4.8 0.7 - - - +
93A GLY* 5.1 4.2 - - - -
94A THR 4.4 6.5 - - - +
96A VAL* 4.0 18.3 - - - +
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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