Contacts of the helix formed by residues 59 - 71 (chain A) in PDB entry 4NFT
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ASN* 4.8 2.5 - - - +
57A THR* 3.4 28.5 - - + +
58A ILE* 1.3 74.8 - - - +
60A SER* 1.3 65.0 + - - +
61A ARG* 3.0 20.0 + - - +
62A GLU* 2.5 34.9 + - - +
63A ILE* 3.3 13.7 + - - +
127A GLY* 4.8 6.1 - - - -
130A ALA* 3.8 9.0 - - - -
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Residues in contact with SER 60 (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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59A THR* 1.3 74.1 - - - +
61A ARG* 1.3 57.6 + - - +
63A ILE* 3.1 11.5 + - - +
64A GLN* 2.8 32.4 + - - +
87A VAL* 4.9 4.2 - - - +
129A THR* 4.3 16.7 + - - -
130A ALA* 3.8 7.8 - - - +
133A TYR* 3.7 35.5 - - - -
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Residues in contact with ARG 61 (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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59A THR* 3.0 12.7 + - - +
60A SER* 1.3 80.9 + - - +
62A GLU* 1.3 65.5 + - + +
64A GLN* 3.6 7.7 + - - +
65A THR* 3.0 32.9 + - - +
68B ARG* 6.0 3.6 - - - +
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Residues in contact with GLU 62 (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 ALA* 3.9 19.9 - - + +
49A LEU* 3.8 28.8 - - + +
50A ALA* 4.0 11.4 - - + +
53A ASN* 3.1 30.2 + - - +
57A THR 4.1 0.4 - - - -
58A ILE* 4.7 1.3 - - + -
59A THR* 2.5 51.5 + - - +
61A ARG* 1.3 85.6 - - - +
63A ILE* 1.3 59.4 + - - +
64A GLN 3.2 0.2 - - - -
65A THR* 3.3 6.6 + - - +
66A ALA* 2.9 29.8 + - - +
69B LEU* 6.1 2.0 - - + -
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Residues in contact with ILE 63 (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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39A PHE* 6.1 0.2 - - + -
42A ILE* 4.0 20.0 - - + -
43A ALA* 5.5 0.2 - - - -
46A ALA* 3.6 25.1 - - + -
58A ILE* 3.8 14.1 - - + -
59A THR 3.5 13.2 - - - +
60A SER* 3.1 9.5 + - - +
62A GLU* 1.3 76.7 - - - +
64A GLN* 1.3 57.9 + - - +
66A ALA* 3.2 2.6 + - - +
67A VAL* 2.8 40.9 + - + +
116A LEU* 4.6 10.5 - - + -
130A ALA* 4.2 10.1 - - + +
133A TYR* 3.6 22.0 - - + -
134A SER* 3.5 29.6 - - - +
137A ILE* 4.6 1.8 - - + -
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Residues in contact with GLN 64 (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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60A SER 2.8 15.3 + - - +
61A ARG* 3.8 9.1 - - - +
63A ILE* 1.3 76.2 - - - +
65A THR* 1.3 64.7 + - - +
67A VAL* 3.5 5.1 + - - +
68A ARG* 3.1 53.4 + - - +
80A VAL* 3.5 19.7 - - + +
84A THR* 4.2 5.2 + - - -
133A TYR* 2.6 38.5 + - - +
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Residues in contact with THR 65 (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 LEU* 3.7 22.4 - - + -
61A ARG* 3.0 20.1 + - - +
62A GLU* 3.7 5.3 - - - -
63A ILE 3.2 0.2 - - - -
64A GLN* 1.3 77.4 - - - +
66A ALA* 1.3 65.8 + - - +
68A ARG* 3.4 7.8 + - - +
69A LEU* 3.0 39.7 + - + +
49B LEU* 6.0 0.4 - - + -
65B THR* 5.4 14.1 - - + +
69B LEU* 5.3 11.1 - - + +
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Residues in contact with ALA 66 (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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42A ILE* 3.6 30.7 - - + +
45A GLU* 3.9 27.1 - - + -
46A ALA* 4.0 4.0 - - - +
49A LEU* 4.1 0.6 - - - +
62A GLU 2.9 17.3 + - - +
63A ILE* 3.5 4.7 - - - +
65A THR* 1.3 76.3 - - - +
67A VAL* 1.3 57.0 + - - +
69A LEU* 3.0 4.7 + - - +
70A LEU* 2.9 37.0 + - + +
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Residues in contact with VAL 67 (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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42A ILE* 3.8 27.4 - - + -
63A ILE* 2.8 34.3 + - + +
64A GLN* 3.7 7.2 - - - +
66A ALA* 1.3 72.7 - - - +
68A ARG* 1.3 57.3 + - - +
70A LEU* 4.9 0.4 - - - -
71A LEU* 2.8 55.5 + - + +
76A ALA* 4.5 3.6 - - - +
79A ALA* 4.3 10.3 - - + -
80A VAL* 4.1 18.8 - - + +
133A TYR* 5.2 0.2 - - + -
137A ILE* 4.0 16.8 - - + -
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Residues in contact with ARG 68 (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 GLN* 3.1 51.3 + - - +
65A THR* 3.9 7.0 - - - +
67A VAL* 1.3 74.8 - - - +
69A LEU* 1.3 61.8 + - + +
71A LEU 3.6 11.3 - - - +
76A ALA* 4.4 14.5 - - + +
77A LYS* 5.2 15.2 - - - +
80A VAL* 3.7 31.6 - - + +
61B ARG* 6.2 2.0 - - - +
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Residues in contact with LEU 69 (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 GLU* 4.0 24.0 - - + +
49A LEU* 4.6 0.9 - - + -
65A THR* 3.0 34.4 + - + +
66A ALA* 3.0 6.7 + - - +
68A ARG* 1.3 81.2 - - + +
70A LEU* 1.3 62.8 + - + +
71A LEU 4.9 0.5 - - - +
49B LEU* 3.8 40.4 - - + +
52B TYR* 3.7 46.8 - - + +
62B GLU* 6.0 2.5 - - + +
65B THR* 5.3 9.2 - - + +
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Residues in contact with LEU 70 (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 ILE* 5.1 3.6 - - + -
41A ARG* 3.4 80.0 + - + +
42A ILE* 3.8 15.7 - - + +
45A GLU* 4.2 10.8 - - + -
66A ALA 2.9 22.6 + - - +
67A VAL* 4.3 2.0 - - - +
69A LEU* 1.3 79.6 - - + +
71A LEU* 1.3 74.3 + - + +
72A PRO* 3.9 4.9 - - - +
179A LEU* 4.8 5.8 - - + +
182A ALA* 5.5 4.3 - - - +
52B TYR* 3.7 22.9 - - + +
54B LYS* 6.0 0.3 + - - -
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Residues in contact with LEU 71 (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 ILE* 4.0 16.8 - - + -
42A ILE* 5.3 2.5 - - + -
67A VAL* 2.8 41.2 + - + +
68A ARG 3.6 14.7 - - - +
69A LEU 4.8 0.7 - - - +
70A LEU* 1.3 82.6 - - + +
72A PRO* 1.3 69.1 - - + +
73A GLY* 3.6 1.9 + - - -
75A LEU* 4.1 15.5 - - + +
76A ALA* 3.8 16.5 - - + +
79A ALA* 4.2 5.4 - - + -
137A ILE* 4.9 2.0 - - + -
141A LEU* 4.0 27.6 - - + -
179A LEU* 3.8 33.9 - - + -
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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