Contacts of the helix formed by residues 61 - 76 (chain B) in PDB entry 5J3V
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 ASP 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B GLU* 1.3 78.8 + - - +
62B GLU* 1.3 59.1 + - - +
63B PRO* 3.2 24.5 - - - +
64B THR* 3.3 20.7 + - - +
65B ARG* 2.6 34.0 + - - +
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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
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60B GLU 3.6 2.5 + - - -
61B ASP* 1.3 74.0 + - - +
63B PRO* 1.4 67.5 - - + +
64B THR 3.1 1.3 - - - -
65B ARG* 3.3 29.5 + - - +
66B SER* 2.8 29.3 + - - -
103B SER* 2.4 38.6 + - - -
105B LEU* 3.6 19.0 - - + +
106B ILE* 3.3 12.3 - - + +
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Residues in contact with PRO 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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61B ASP* 3.2 21.5 - - - +
62B GLU* 1.4 93.7 - - + +
64B THR* 1.3 56.2 + - - +
66B SER* 4.0 1.9 - - - -
67B LEU* 3.0 30.2 + - - +
105B LEU* 4.3 14.1 - - + -
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Residues in contact with THR 64 (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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53B VAL* 3.9 12.0 - - + +
60B GLU* 5.6 3.4 - - + -
61B ASP* 3.3 26.6 + - - +
62B GLU 3.1 0.4 - - - -
63B PRO* 1.3 74.5 - - - +
65B ARG* 1.3 64.8 + - - +
66B SER 3.1 2.8 + - - -
67B LEU* 4.4 9.2 - - + -
68B SER* 3.3 26.0 + - - -
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Residues in contact with ARG 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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53B VAL* 3.1 30.5 - - + +
54B LEU* 2.7 41.1 + - - +
55B THR* 4.4 1.6 + - - +
57B LEU 3.5 21.2 + - - -
58B LYS* 3.2 35.1 - - - +
59B SER 5.3 0.2 - - - +
60B GLU* 4.3 13.2 - - + +
61B ASP 2.6 20.5 + - - +
62B GLU* 3.1 34.9 + - - +
64B THR* 1.3 73.6 - - - +
66B SER* 1.3 59.2 + - - +
68B SER* 3.9 3.8 + - - -
69B GLY 4.1 0.5 + - - -
101B ASP* 3.1 27.1 + - - -
103B SER* 5.3 0.2 - - - -
106B ILE* 3.3 19.1 - - + +
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Residues in contact with SER 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 4.5 1.1 - - - -
62B GLU 2.8 15.4 + - - -
63B PRO* 4.1 2.7 - - - -
65B ARG* 1.3 78.3 - - - +
67B LEU* 1.3 64.0 + - - +
68B SER 3.3 2.5 - - - -
69B GLY* 2.9 11.4 + - - -
70B LEU* 3.0 26.3 + - - +
105B LEU* 3.2 27.9 - - - +
106B ILE* 4.7 2.2 - - - -
109B THR* 2.6 31.3 + - - +
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Residues in contact with LEU 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 PRO 3.0 20.0 + - - +
64B THR* 3.5 9.1 + - + +
66B SER* 1.3 77.9 - - - +
68B SER* 1.3 56.3 + - - +
70B LEU* 3.0 28.0 + - + +
71B ILE* 3.1 33.7 + - + +
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Residues in contact with SER 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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50B LEU* 3.2 49.3 + - - +
53B VAL* 3.6 25.0 + - - +
64B THR* 3.3 18.8 + - - -
65B ARG 3.9 3.3 + - - -
67B LEU* 1.3 78.6 - - - +
69B GLY* 1.3 59.3 + - - +
70B LEU 3.2 1.2 + - - -
71B ILE* 3.8 12.9 + - - -
72B LEU* 3.7 8.7 + - - +
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Residues in contact with GLY 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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50B LEU 4.7 1.6 - - - -
54B LEU* 4.1 20.9 - - - -
65B ARG 4.1 1.0 + - - -
66B SER 2.9 12.9 + - - -
68B SER* 1.3 79.8 + - - +
70B LEU* 1.3 57.6 + - - +
71B ILE 3.6 0.2 - - - -
72B LEU* 4.0 8.4 - - - +
109B THR* 3.7 17.2 - - - +
113B LEU* 3.6 29.6 - - - +
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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
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66B SER* 3.0 30.3 + - - +
67B LEU* 3.0 16.5 + - + +
69B GLY* 1.3 78.4 - - - +
71B ILE* 1.3 60.4 + - - +
72B LEU 3.2 1.3 - - - -
73B LYS* 3.2 19.5 + - + +
74B ASN* 3.2 21.5 - - - +
105B LEU* 5.8 1.3 - - + -
109B THR* 4.0 18.2 - - + +
112B ILE* 4.1 23.3 - - + -
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Residues in contact with ILE 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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37B LEU* 3.6 39.3 - - + +
50B LEU* 4.1 23.8 - - + -
67B LEU* 3.2 33.4 - - + +
68B SER* 3.8 11.4 + - - +
70B LEU* 1.3 74.8 - - - +
72B LEU* 1.3 55.0 + - - +
73B LYS 3.1 1.3 - - - -
74B ASN* 2.9 11.6 + - + +
75B ASN* 2.7 47.7 + - - +
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Residues in contact with LEU 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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47B ASN* 4.6 5.8 - - - +
50B LEU* 4.0 10.2 - - + +
51B ILE* 3.7 39.7 - - + +
68B SER 3.7 9.7 + - - +
69B GLY* 4.0 12.1 - - - +
71B ILE* 1.3 80.3 - - - +
73B LYS* 1.3 55.1 + - - +
74B ASN 3.1 0.2 - - - -
75B ASN* 3.7 7.4 - - + +
76B VAL* 3.1 54.1 + - + +
83B PHE* 5.4 1.6 - - + -
91B ILE* 3.7 40.6 - - + -
113B LEU* 3.7 19.3 - - + -
117B ILE* 4.0 3.6 - - + -
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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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70B LEU* 3.2 21.8 + - + +
71B ILE 3.1 0.6 - - - -
72B LEU* 1.3 78.3 - - - +
74B ASN* 1.3 68.6 + - - +
76B VAL* 5.0 2.5 - - - -
77B LYS* 3.1 42.5 + - + +
112B ILE* 4.1 25.4 - - + -
113B LEU* 3.8 16.2 - - + +
116B THR* 3.6 39.9 + - - +
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Residues in contact with ASN 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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38B GLU* 5.3 1.0 - - - +
70B LEU 3.2 12.8 - - - +
71B ILE* 2.9 18.2 + - + +
73B LYS* 1.3 95.0 + - - +
75B ASN* 1.3 62.8 + - - +
76B VAL 3.4 1.8 - - - -
77B LYS* 4.2 10.2 - - - +
78B ALA* 3.7 9.5 + - - +
79B HIS* 3.2 19.6 + - - -
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Residues in contact with ASN 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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37B LEU 4.3 14.2 + - - +
38B GLU* 5.0 3.8 - - - +
41B ASN* 3.1 20.6 + - - +
47B ASN* 3.0 28.9 + - - +
50B LEU* 4.1 11.3 - - - +
71B ILE* 2.7 26.7 + - - +
72B LEU* 3.3 6.9 + - - +
74B ASN* 1.3 79.2 - - - +
76B VAL* 1.3 61.3 + - + +
78B ALA 2.9 15.0 - - - +
79B HIS* 3.2 27.9 + - - +
80B PHE* 4.7 0.5 - - - -
83B PHE* 4.2 10.9 - - + -
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Residues in contact with VAL 76 (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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72B LEU* 3.1 36.2 + - + +
73B LYS* 5.0 2.0 - - - -
75B ASN* 1.3 82.7 - - - +
77B LYS* 1.3 66.1 + - - +
78B ALA 3.1 4.7 + - - +
80B PHE* 3.7 40.3 - - + +
83B PHE* 4.3 18.2 - - + -
91B ILE* 5.8 0.2 - - + -
116B THR 3.7 11.7 - - - +
117B ILE* 3.6 30.5 - - + -
120B LYS* 3.9 16.1 - - + +
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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