Contacts of the helix formed by residues 59 - 71 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D ASN* 4.8 2.7 - - - +
57D THR* 3.9 24.2 - - + +
58D ILE* 1.3 75.6 - - - +
60D SER* 1.3 61.1 + - - +
61D ARG* 3.1 17.8 + - - +
62D GLU* 2.5 42.6 + - - +
63D ILE* 3.0 17.6 + - - +
127D GLY* 4.8 7.4 - - - -
130D ALA* 4.3 4.3 - - - -
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Residues in contact with SER 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D THR* 1.3 72.6 - - - +
61D ARG* 1.3 60.5 + - - +
63D ILE* 3.6 10.6 - - - +
64D GLN* 2.7 35.7 + - - +
129D THR* 3.5 16.4 + - - -
130D ALA* 4.4 6.3 - - - +
133D TYR* 3.3 43.7 - - - -
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D THR* 3.1 13.4 + - - +
60D SER* 1.3 83.0 + - - +
62D GLU* 1.3 68.5 + - - +
64D GLN* 3.6 25.0 + - - +
65D THR* 3.1 29.0 + - + +
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ALA* 3.8 21.9 - - + +
49D LEU* 3.8 17.3 - - + +
50D ALA* 3.8 24.5 - - + +
53D ASN* 3.1 26.9 + - - +
57D THR 4.3 0.2 - - - -
58D ILE* 5.0 0.4 - - + -
59D THR* 2.5 44.9 + - - +
61D ARG* 1.3 79.1 - - - +
63D ILE* 1.3 66.9 + - - +
65D THR* 3.4 5.1 + - - -
66D ALA* 3.0 24.4 + - - +
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ILE* 4.3 13.2 - - + -
46D ALA* 4.0 19.3 - - + -
58D ILE* 4.1 12.8 - - + -
59D THR 3.0 16.6 + - - +
60D SER* 3.2 13.2 + - - +
62D GLU* 1.3 73.6 - - - +
64D GLN* 1.3 67.3 + - - +
66D ALA* 3.2 3.7 + - - +
67D VAL* 2.9 36.4 + - + +
116D LEU* 4.1 13.2 - - + -
130D ALA* 4.4 8.3 - - + +
133D TYR* 4.7 8.1 - - + -
134D SER* 3.4 27.6 - - - +
137D ILE* 4.3 13.2 - - + -
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Residues in contact with GLN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D SER 2.7 21.1 + - - +
61D ARG* 3.6 27.3 + - - +
63D ILE* 1.3 76.1 - - - +
65D THR* 1.3 66.5 + - + +
67D VAL* 3.1 4.1 + - - +
68D ARG* 2.9 37.7 + - + +
80D VAL* 3.8 42.0 - - + +
133D TYR* 6.3 3.6 - - + -
137D ILE* 5.8 0.4 - - - -
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Residues in contact with THR 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU* 3.2 22.3 - - + +
61D ARG* 3.1 19.7 + - + +
62D GLU* 4.3 5.4 - - + +
63D ILE 3.3 0.4 - - - -
64D GLN* 1.3 79.4 - - + +
66D ALA* 1.3 61.1 - - - +
68D ARG* 3.1 22.1 + - - +
69D LEU* 3.0 29.5 + - - +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ILE* 3.6 33.2 - - + +
45D GLU* 3.9 19.1 - - + +
46D ALA* 3.8 14.1 - - + +
49D LEU* 4.0 1.7 - - + +
62D GLU 3.0 18.7 + - - +
63D ILE 3.5 3.6 - - - +
65D THR* 1.3 78.8 + - - +
67D VAL* 1.3 61.2 + - - +
69D LEU* 3.0 14.9 + - - +
70D LEU* 3.2 12.8 + - - +
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ILE* 3.8 27.8 - - + -
63D ILE* 2.9 23.0 + - + +
64D GLN* 3.4 9.4 - - - +
66D ALA* 1.3 76.5 - - - +
68D ARG* 1.3 57.9 + - - +
70D LEU* 3.1 2.3 + - - +
71D LEU* 3.0 53.8 + - + +
76D ALA* 4.3 13.6 - - + +
79D ALA* 4.8 0.4 - - + -
80D VAL* 4.5 12.1 - - + -
137D ILE* 3.7 30.3 - - + -
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Residues in contact with ARG 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLN* 2.9 37.4 + - + +
65D THR* 3.1 22.4 + - - +
67D VAL* 1.3 75.8 - - + +
69D LEU* 1.3 60.8 + - + +
71D LEU 3.5 11.8 - - - +
76D ALA* 4.5 18.4 - - + -
77D LYS* 5.3 17.4 - - - +
80D VAL* 5.7 2.0 - - + -
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ARG* 4.6 10.0 + - - +
45D GLU* 3.8 36.3 - - + +
49D LEU* 4.6 7.9 - - + -
65D THR* 3.0 24.2 + - - +
66D ALA* 3.0 9.6 + - - +
68D ARG* 1.3 80.8 - - + +
70D LEU* 1.3 57.2 + - - +
182D ALA* 5.9 0.3 - - - +
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ILE* 4.0 26.5 - - + +
41D ARG* 4.3 26.9 - - + +
42D ILE* 4.4 10.8 - - + -
66D ALA 3.2 8.3 + - - +
67D VAL* 3.1 6.5 + - - +
69D LEU* 1.3 81.0 - - - +
71D LEU* 1.3 84.3 + - + +
72D PRO* 3.9 3.8 - - - +
179D LEU* 3.9 13.2 - - + +
182D ALA* 3.7 40.2 - - + +
183D THR* 3.9 15.9 - - - +
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ILE* 5.3 2.9 - - + -
67D VAL* 3.0 34.4 + - + +
68D ARG 3.5 15.6 - - - +
69D LEU 5.0 0.2 - - - -
70D LEU* 1.3 103.8 - - + +
72D PRO* 1.3 80.8 - - + +
73D GLY* 3.6 1.6 + - - -
75D LEU* 4.0 9.6 - - + -
76D ALA* 4.1 19.6 - - + +
79D ALA* 4.2 9.2 - - + -
137D ILE* 5.2 0.4 - - + -
141D LEU* 3.9 35.2 - - + -
179D LEU* 3.7 15.9 - - + -
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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