Contacts of the helix formed by residues 59 - 75 (chain B) in PDB entry 3Q2T
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 SER 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B SER* 1.3 89.1 + - - +
60B VAL* 1.3 77.8 + - - +
61B ALA* 3.9 7.7 + - - +
62B ALA* 3.3 20.9 - - - +
63B ARG* 3.7 9.4 + - - -
4F U 3.9 4.9 - - - -
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Residues in contact with VAL 60 (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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59B SER* 1.3 77.8 + - - +
61B ALA* 1.3 57.9 + - - +
62B ALA 2.8 10.9 + - - -
63B ARG* 3.3 35.1 + - - +
64B PHE* 3.9 13.4 + - + -
3F G 4.5 9.6 - - + +
4F U 3.9 27.6 - - + +
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER* 3.9 6.0 + - - +
60B VAL* 1.3 77.9 - - - +
62B ALA* 1.3 56.3 + - - +
64B PHE* 4.1 9.1 - - - +
65B GLN* 3.0 31.9 + - - +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP* 4.0 6.5 - - + +
58B SER* 4.0 19.5 - - - +
59B SER* 3.3 25.7 + - - +
60B VAL 2.8 2.6 + - - -
61B ALA* 1.3 75.1 - - - +
63B ARG* 1.3 55.3 + - - +
65B GLN* 2.9 13.4 + - - +
66B ARG* 2.7 34.1 + - - +
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU* 5.1 6.9 + - - +
57B ASP* 3.0 42.5 + - - +
58B SER 3.8 5.7 + - - -
59B SER 3.7 10.1 + - - -
60B VAL* 3.3 22.2 + - - +
62B ALA* 1.3 78.6 - - - +
64B PHE* 1.3 79.5 + - + +
66B ARG* 3.5 1.7 - - - +
67B MET* 2.5 46.1 + - + +
77B ARG* 3.7 8.4 + - - +
150B ARG* 6.1 3.1 - - - +
3F G 3.6 35.0 + - - +
4F U 3.2 25.1 + - - -
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Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 4.2 16.8 - - + -
61B ALA* 3.8 10.3 + - - +
62B ALA 3.1 0.4 - - - -
63B ARG* 1.3 94.0 - - + +
65B GLN* 1.3 57.7 + - - +
67B MET* 3.2 25.2 - - + +
68B ARG* 2.6 41.0 + - + +
150B ARG* 3.7 13.5 - - - -
153B PHE* 3.2 35.6 - - + +
154B GLU* 3.1 39.0 - - - -
155B PRO* 3.5 13.0 - - + -
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Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA* 3.0 20.2 + - - +
62B ALA* 2.9 9.8 + - - +
64B PHE* 1.3 75.2 - - - +
66B ARG* 1.3 57.5 + - - +
68B ARG* 3.6 7.3 - - - +
69B GLU* 2.9 58.3 + - + +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LYS* 3.6 29.4 - - - +
57B ASP* 2.5 48.4 + - - +
62B ALA 2.7 12.8 + - - +
63B ARG 3.6 2.9 - - - +
65B GLN* 1.3 72.2 - - - +
67B MET* 1.3 53.0 + - - +
69B GLU* 3.4 13.9 - - - +
70B GLU* 2.6 77.6 + - + +
77B ARG* 2.8 22.7 - - - +
110B GLU* 2.5 44.6 + - - -
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Residues in contact with MET 67 (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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63B ARG* 2.5 38.6 + - + +
64B PHE* 3.0 36.2 + - + +
66B ARG* 1.3 72.4 - - - +
68B ARG* 1.3 66.0 + - - +
70B GLU* 3.6 2.8 - - - +
71B PHE* 2.8 27.2 + - + +
77B ARG* 4.0 39.2 - - + +
150B ARG* 4.0 25.4 - - - +
153B PHE* 3.8 18.8 - - + -
169B LYS* 4.5 9.2 - - + -
170B GLU* 4.3 15.7 - - - +
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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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64B PHE* 2.6 20.8 + - + +
65B GLN* 3.6 7.2 - - - +
67B MET* 1.3 72.9 - - - +
69B GLU* 1.3 69.2 + - + +
71B PHE* 3.3 4.0 + - - +
72B ASP* 3.2 18.7 + - - +
153B PHE* 3.4 62.6 - - + +
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Residues in contact with GLU 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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65B GLN* 2.9 60.0 + - + +
66B ARG* 3.4 15.5 - - - +
68B ARG* 1.3 72.9 - - + +
70B GLU* 1.3 67.7 + - + +
72B ASP* 2.8 25.1 + - - +
73B LYS* 3.7 8.6 + - - +
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Residues in contact with GLU 70 (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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56B LYS* 5.0 5.5 + - - -
66B ARG* 2.6 71.6 + - + +
67B MET* 3.7 2.2 - - - +
69B GLU* 1.3 72.7 - - + +
71B PHE* 1.3 54.7 + - - +
72B ASP 3.0 0.9 + - - -
73B LYS* 3.0 8.2 + - - +
74B ILE* 2.7 63.6 + - + +
77B ARG* 3.5 23.9 + - + +
110B GLU* 4.2 2.8 - - - +
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Residues in contact with PHE 71 (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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67B MET* 2.8 21.7 + - + +
68B ARG 3.5 4.5 - - - +
70B GLU* 1.3 73.4 - - - +
72B ASP* 1.3 67.5 + - - +
75B GLY* 2.5 59.5 + - - +
76B MET* 3.3 25.1 - - + -
77B ARG* 5.5 2.4 - - + +
153B PHE* 4.1 21.3 - + + -
167B LYS* 4.8 17.7 - - + -
168B PRO 3.9 15.5 - - - -
169B LYS* 4.0 29.6 - - + +
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Residues in contact with ASP 72 (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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68B ARG 3.2 8.3 + - - +
69B GLU* 2.8 22.1 + - - +
71B PHE* 1.3 82.4 - - - +
73B LYS* 1.3 55.6 + - + +
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Residues in contact with LYS 73 (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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69B GLU* 4.0 9.2 - - + +
70B GLU* 3.4 13.5 - - - +
72B ASP* 1.3 76.9 - - + +
74B ILE* 1.3 71.2 + - + +
75B GLY 3.5 0.4 - - - -
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Residues in contact with ILE 74 (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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70B GLU* 2.7 58.0 + - + +
73B LYS* 1.3 85.2 - - + +
75B GLY* 1.3 63.8 + - - +
76B MET 4.5 8.9 - - - +
77B ARG* 5.9 1.3 - - - -
113B PRO* 3.5 39.5 - - + +
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Residues in contact with GLY 75 (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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71B PHE* 2.5 51.9 + - - -
73B LYS 3.5 1.2 - - - -
74B ILE* 1.3 77.5 - - - +
76B MET* 1.3 69.1 - - - +
77B ARG* 3.5 1.4 + - - +
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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