Contacts of the helix formed by residues 59 - 71 (chain B) in PDB entry 3UDB
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 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A VAL* 4.4 6.1 - - - +
56B GLU 4.7 5.3 - - - +
57B LYS* 3.4 14.1 - - - +
58B ILE* 1.3 80.0 - - - +
60B GLU* 1.3 66.5 + - - +
61B ASN* 3.7 21.8 + - - +
62B VAL* 3.4 21.7 + - - +
63B LYS* 3.6 17.5 + - - +
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Residues in contact with GLU 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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64A ARG* 3.2 30.3 + - + +
68A ASN* 3.8 3.5 + - - -
136A VAL* 3.8 14.6 - - + +
137A ALA* 4.2 24.4 - - + +
59B ASP* 1.3 75.4 - - - +
61B ASN* 1.3 56.7 + - - +
63B LYS* 2.4 50.5 + - - +
64B ARG* 2.7 35.1 + - - +
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Residues in contact with ASN 61 (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 ASP* 3.7 20.4 + - - +
60B GLU* 1.3 77.0 - - - +
62B VAL* 1.3 66.1 + - + +
64B ARG* 1.6 43.8 + - - +
65B GLU* 3.0 33.6 + - - +
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Residues in contact with VAL 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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52B ILE* 3.7 37.0 - - + -
57B LYS* 4.3 10.8 - - + +
58B ILE* 4.6 15.5 - - + -
59B ASP* 3.4 22.4 + - - +
60B GLU 3.5 0.2 - - - -
61B ASN* 1.3 79.2 - - + +
63B LYS* 1.3 63.4 + - - +
65B GLU* 3.4 15.1 + - - +
66B ILE* 3.0 40.0 + - + +
90B LEU* 4.7 3.4 - - + -
92B ILE* 5.1 0.2 - - + -
163B TYR* 5.1 2.0 - - + -
312B ILE* 5.5 2.0 - - + -
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Residues in contact with LYS 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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64A ARG* 4.3 8.3 - - - +
68A ASN* 2.8 34.8 + - - +
136A VAL* 4.1 17.3 - - + +
139A ARG* 5.6 0.2 - - - +
59B ASP 3.6 12.8 + - - +
60B GLU* 2.4 50.7 + - - +
61B ASN 3.2 0.2 - - - -
62B VAL* 1.3 80.9 - - - +
64B ARG* 1.3 66.6 + - - +
66B ILE* 3.4 1.3 + - - +
67B ILE* 3.1 45.2 + - + +
309B MET* 4.0 15.0 - - - -
312B ILE* 3.8 28.5 - - + -
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Residues in contact with ARG 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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60A GLU* 3.3 30.4 + - - +
63A LYS* 4.1 4.9 - - - +
64A ARG* 6.2 6.1 - - + -
60B GLU 2.7 20.9 + - - +
61B ASN* 1.6 46.7 + - - +
63B LYS* 1.3 78.1 - - - +
65B GLU* 1.3 86.4 + - - +
67B ILE* 3.7 5.5 - - - +
68B ASN* 3.0 40.0 + - - +
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Residues in contact with GLU 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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61B ASN* 3.0 20.6 + - - +
62B VAL* 3.7 14.9 - - - +
64B ARG* 1.3 93.0 + - - +
66B ILE* 1.3 64.1 + - - +
68B ASN* 3.2 9.1 + - - +
69B HIS* 2.8 25.8 + - - +
162B GLY* 2.2 38.0 - - - +
163B TYR* 3.6 26.9 - - + -
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Residues in contact with ILE 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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62B VAL* 3.0 23.1 + - + +
63B LYS 3.7 4.7 - - - +
64B ARG 3.4 0.2 - - - -
65B GLU* 1.3 78.4 - - - +
67B ILE* 1.3 58.2 + - - +
69B HIS* 3.5 1.9 + - - +
70B ARG* 2.9 26.7 + - + +
80B PHE* 3.9 21.3 - - + -
83B VAL* 3.9 19.5 - - + -
90B LEU* 4.1 17.5 - - + -
92B ILE* 4.1 10.1 - - + -
163B TYR* 3.9 25.1 - - + +
308B ILE* 4.1 24.9 - - + -
312B ILE* 3.8 19.3 - - + -
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Residues in contact with ILE 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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63A LYS* 5.9 2.5 - - + -
67A ILE* 3.8 42.0 - - + -
305A ILE* 4.0 10.6 - - + +
309A MET* 4.8 4.3 - - + -
63B LYS* 3.1 48.2 + - + +
64B ARG* 3.7 5.4 - - - +
66B ILE* 1.3 73.3 - - - +
68B ASN* 1.3 72.3 + - - +
70B ARG* 2.9 18.0 + - + +
71B SER* 3.1 12.8 + - - -
305B ILE* 4.9 7.9 - - + -
308B ILE* 4.7 11.0 - - + -
309B MET* 3.8 19.5 - - + -
312B ILE* 4.4 8.1 - - + -
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Residues in contact with ASN 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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60A GLU* 4.1 3.3 + - - +
63A LYS* 3.5 19.2 + - - +
309A MET* 2.6 38.8 - - - +
64B ARG* 3.0 34.6 + - - +
65B GLU* 3.4 7.2 - - - +
67B ILE* 1.3 80.2 - - - +
69B HIS* 1.3 61.5 + - - +
71B SER* 2.7 25.3 + - - -
72B LEU* 3.7 8.7 - - - +
139B ARG* 3.8 33.0 + - - +
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Residues in contact with HIS 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 GLU 2.8 15.9 + - - +
66B ILE 3.8 1.8 - - - +
68B ASN* 1.3 73.4 - - - +
70B ARG* 1.3 62.6 + - - +
72B LEU* 3.2 27.1 + - + +
78B VAL 2.5 30.5 + - - -
79B ARG* 4.8 0.4 - - - -
80B PHE* 3.4 26.7 + - + +
94B MET* 4.0 24.0 - - + -
139B ARG* 6.1 0.2 - - - +
160B ASP 4.0 10.5 + - - +
161B PHE* 3.6 28.8 - + + +
163B TYR* 2.7 31.1 + - + +
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Residues in contact with ARG 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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305A ILE* 3.5 23.1 - - + +
306A GLU* 3.3 28.3 + - - +
66B ILE* 2.9 18.5 + - + +
67B ILE* 2.9 12.5 + - + +
69B HIS* 1.3 78.4 - - - +
71B SER* 1.3 57.6 + - - +
72B LEU 3.3 4.0 + - - +
73B ARG* 5.6 1.4 - - - +
80B PHE* 3.6 28.9 - - + +
302B GLY* 3.2 29.9 + - - +
303B GLN* 2.4 33.2 + - - +
304B SER* 4.6 1.2 - - - +
305B ILE 5.5 1.3 - - - +
308B ILE* 3.6 22.9 - - + -
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Residues in contact with SER 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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305A ILE* 3.5 31.9 - - - -
306A GLU* 3.3 18.4 - - - +
309A MET* 3.7 30.5 - - - +
67B ILE 3.1 8.1 + - - -
68B ASN 2.7 19.4 + - - -
69B HIS 3.1 0.2 - - - -
70B ARG* 1.3 76.8 - - - +
72B LEU* 1.3 62.9 + - - +
73B ARG 3.3 3.5 + - - -
130B TYR* 3.4 9.0 + - - -
134B MET* 4.1 8.4 + - - +
139B ARG* 5.3 0.3 + - - -
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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