Contacts of the helix formed by residues 59 - 71 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B ASN* 4.8 3.1 - - - +
57B THR* 3.4 28.3 - - + +
58B ILE* 1.3 75.3 - - - +
60B SER* 1.3 66.1 + - - +
61B ARG* 3.0 19.6 + - - +
62B GLU* 2.6 35.9 + - - +
63B ILE* 3.3 13.0 + - - +
127B GLY* 4.7 6.5 - - - -
130B ALA* 3.8 8.1 - - - -
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 1.3 75.0 + - - +
61B ARG* 1.3 58.4 + - - +
63B ILE* 3.1 11.8 + - - +
64B GLN* 2.8 33.3 + - - +
87B VAL* 4.9 4.3 - - - +
129B THR* 4.3 16.4 + - - -
130B ALA* 3.9 7.8 - - - +
133B TYR* 3.7 35.4 - - - -
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 6.2 1.8 - - - +
59B THR* 3.0 12.8 + - - +
60B SER* 1.3 81.8 + - - +
62B GLU* 1.3 67.5 + - + +
64B GLN* 3.6 11.7 + - - +
65B THR* 3.1 36.3 + - + +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 6.0 3.2 - - + +
46B ALA* 3.8 19.2 - - + +
49B LEU* 3.9 28.8 - - + +
50B ALA* 4.0 12.8 - - + +
53B ASN* 3.0 29.9 + - - +
57B THR 4.1 0.7 - - - -
58B ILE* 4.7 0.9 - - + -
59B THR* 2.6 50.7 + - - +
61B ARG* 1.3 82.4 - - + +
63B ILE* 1.3 62.0 + - - +
64B GLN 3.2 0.2 - - - -
65B THR* 3.3 8.1 + - - +
66B ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PHE* 6.1 0.2 - - + -
42B ILE* 4.1 18.6 - - + -
43B ALA* 5.5 0.2 - - - -
46B ALA* 3.6 22.7 - - + -
58B ILE* 3.8 14.1 - - + -
59B THR 3.5 12.8 - - - +
60B SER* 3.1 9.5 + - - +
62B GLU* 1.3 76.1 - - - +
64B GLN* 1.3 57.9 + - - +
66B ALA* 3.2 4.9 + - - +
67B VAL* 2.8 34.4 + - + +
116B LEU* 4.5 11.2 - - + -
130B ALA* 4.2 10.1 - - + +
133B TYR* 3.6 22.2 - - + -
134B SER* 3.6 29.6 - - - +
137B ILE* 4.7 2.0 - - + -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B SER 2.8 15.7 + - - +
61B ARG* 3.7 11.8 + - - +
62B GLU 3.2 0.2 - - - -
63B ILE* 1.3 78.3 - - - +
65B THR* 1.3 60.7 + - + +
67B VAL* 3.5 5.1 + - - +
68B ARG* 3.1 54.0 + - - +
80B VAL* 3.3 20.7 - - + +
84B THR* 4.1 5.4 + - - -
133B TYR* 2.6 38.2 + - + +
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A THR* 5.4 12.4 - - + +
69A LEU* 5.3 8.5 - - + +
49B LEU* 3.1 26.3 - - - +
61B ARG* 3.1 27.2 + - + +
62B GLU* 3.3 2.4 + - - -
63B ILE 3.3 0.4 - - - -
64B GLN* 1.3 79.1 - - + +
66B ALA* 1.3 65.3 + - - +
68B ARG* 3.4 9.1 + - - +
69B LEU* 3.0 33.6 + - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ILE* 3.7 31.0 - - + +
45B GLU* 3.9 27.1 - - + -
46B ALA* 4.0 3.6 - - - +
49B LEU* 4.1 0.4 - - + +
62B GLU 2.9 18.0 + - - +
63B ILE* 3.5 5.4 - - - +
65B THR* 1.3 77.9 + - - +
67B VAL* 1.3 58.0 + - - +
69B LEU* 3.0 5.1 + - - +
70B LEU* 2.9 34.5 + - - +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.9 27.4 - - + -
63B ILE* 2.8 29.2 + - + +
64B GLN* 3.7 7.0 - - - +
66B ALA* 1.3 72.0 - - - +
68B ARG* 1.3 57.8 + - - +
70B LEU* 4.9 0.4 - - - -
71B LEU* 2.8 55.8 + - + +
76B ALA* 4.5 3.4 - - - +
79B ALA* 4.4 9.6 - - + -
80B VAL* 4.2 19.3 - - + +
133B TYR* 5.2 0.2 - - + -
137B ILE* 4.0 22.2 - - + -
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Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 6.0 3.6 - - - +
64B GLN* 3.1 47.5 + - - +
65B THR* 3.9 7.8 - - - +
66B ALA 3.3 0.2 - - - -
67B VAL* 1.3 77.2 - - - +
69B LEU* 1.3 62.4 + - + +
71B LEU 3.6 11.4 - - - +
76B ALA* 4.5 13.1 - - + +
77B LYS* 5.2 16.0 - - - +
80B VAL* 3.7 34.0 - - + +
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Residues in contact with LEU 69 (chain B).
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* 3.8 38.8 - - + +
52A TYR* 3.8 45.9 - - + +
62A GLU* 6.1 1.8 - - + -
65A THR* 5.3 11.0 - - + +
45B GLU* 4.0 25.6 - - + +
49B LEU* 4.5 1.8 - - + -
65B THR* 3.0 30.7 + - - +
66B ALA* 3.0 5.4 + - - +
68B ARG* 1.3 79.7 - - + +
70B LEU* 1.3 62.1 + - + +
71B LEU 4.8 0.7 - - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 3.6 23.1 - - + +
38B ILE* 5.2 4.0 - - + -
41B ARG* 3.4 80.1 + - + +
42B ILE* 3.7 16.8 - - + +
45B GLU* 4.2 9.6 - - + -
66B ALA 2.9 20.8 + - - +
67B VAL* 4.3 1.8 - - - +
69B LEU* 1.3 79.0 - - + +
71B LEU* 1.3 73.3 + - + +
72B PRO* 3.9 4.9 - - - +
179B LEU* 4.6 7.1 - - - +
182B ALA* 5.7 3.5 - - - +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 4.1 15.3 - - + -
42B ILE* 5.3 2.7 - - + -
67B VAL* 2.8 38.7 + - + +
68B ARG 3.6 13.7 - - - +
69B LEU 4.8 0.9 - - - +
70B LEU* 1.3 83.8 - - + +
72B PRO* 1.3 70.5 - - + +
73B GLY* 3.6 1.7 + - - -
75B LEU* 4.0 21.8 - - + +
76B ALA* 3.8 14.5 - - + +
79B ALA* 4.2 5.6 - - + -
137B ILE* 5.0 1.8 - - + -
141B LEU* 4.1 24.0 - - + -
179B LEU* 3.9 33.0 - - + -
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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