Contacts of the helix formed by residues 67 - 85 (chain A) in PDB entry 5UDJ
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 GLN 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A LYS* 2.9 31.6 + - - +
63A HIS 4.2 0.2 + - - -
65A LYS* 3.4 44.2 + - - +
66A GLY* 1.3 78.8 - - - +
68A ASN* 1.3 60.6 + - - +
69A GLU 3.3 2.9 - - - -
70A GLU* 3.2 22.4 + - + +
71A ALA* 2.9 23.6 + - - +
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A HIS* 2.8 39.3 + - - +
66A GLY* 3.7 5.6 + - - -
67A GLN* 1.3 77.4 - - - +
69A GLU* 1.3 63.8 + - - +
71A ALA* 3.2 3.7 + - - +
72A LEU* 3.0 26.6 + - - +
104A MET* 3.2 20.6 - - + +
107A HIS* 4.9 8.5 + - - +
108A MET* 3.8 28.7 - - + +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN 3.3 0.2 - - - -
68A ASN* 1.3 76.7 - - + +
70A GLU* 1.3 67.1 + - + +
72A LEU* 3.4 19.2 + - - +
73A LYS* 3.3 27.4 + - - +
108A MET* 3.5 22.6 - - + +
110A ARG* 4.2 8.8 + - - -
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 4.2 18.9 - - + +
67A GLN* 3.2 35.9 + - + +
69A GLU* 1.3 76.9 - - + +
71A ALA* 1.3 65.6 + - - +
73A LYS* 2.9 51.6 + - - +
74A SER* 3.2 14.4 + - - -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ALA* 3.2 37.3 - - + +
62A LYS* 3.7 8.0 - - - +
63A HIS 3.9 6.5 - - - +
67A GLN 2.9 13.5 + - - +
68A ASN 3.2 8.9 + - - +
70A GLU* 1.3 76.6 - - - +
72A LEU* 1.3 62.6 + - - +
74A SER 3.1 10.4 + - - -
75A LEU* 3.1 12.0 + - - +
104A MET* 3.7 21.8 - - + -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN 3.0 15.5 + - - +
69A GLU* 3.7 20.6 - - - +
70A GLU 3.3 0.2 - - - -
71A ALA* 1.3 77.3 - - - +
73A LYS* 1.3 62.8 + - - +
75A LEU* 3.2 5.5 + - + +
76A LYS* 3.0 41.6 + - - +
101A PHE* 4.0 13.1 - - + -
104A MET* 3.9 25.1 - - + -
105A TYR* 3.7 29.6 - - + +
108A MET* 3.7 16.4 - - + -
110A ARG* 3.7 26.7 - - - +
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU* 3.3 14.3 + - - +
70A GLU* 2.9 43.7 + - - +
72A LEU* 1.3 79.2 - - + +
74A SER* 1.3 56.3 + - - +
76A LYS* 3.4 10.6 + - + +
77A GLU* 3.0 28.6 + - - +
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A HIS* 3.7 26.8 + - - +
58A LEU* 3.6 26.0 - - - +
59A ALA* 3.8 11.2 - - - -
62A LYS* 4.9 3.1 - - - +
70A GLU 3.2 7.3 + - - -
71A ALA 3.1 9.8 + - - -
73A LYS* 1.3 74.9 - - - +
75A LEU* 1.3 61.5 + - - +
77A GLU* 3.3 13.7 + - - +
78A ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASN* 3.2 31.2 - - - +
59A ALA* 3.6 19.7 - - + -
71A ALA 3.1 18.2 + - - +
72A LEU* 3.2 7.6 + - + +
74A SER* 1.3 75.9 - - - +
76A LYS* 1.3 62.8 + - - +
78A ALA* 3.2 6.7 + - - +
79A GLU* 3.1 25.5 + - - +
97A THR* 3.7 5.2 - - + +
100A ASN* 3.8 15.3 - - + -
101A PHE* 3.6 55.2 - - + +
104A MET* 3.9 18.4 - - + -
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.0 30.0 + - - +
73A LYS* 3.7 9.4 - - + +
75A LEU* 1.3 77.5 - - - +
77A GLU* 1.3 55.6 + - - +
79A GLU* 3.3 7.1 + - - +
80A ASN* 2.9 39.3 + - - +
101A PHE* 3.9 15.7 - - + -
105A TYR* 4.5 16.6 + - - -
110A ARG* 5.9 2.6 - - - +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 5.9 0.3 - - - +
55A HIS* 3.7 30.2 + - + +
58A LEU* 6.1 0.5 - - - +
73A LYS 3.0 18.2 + - - +
74A SER* 3.6 11.9 + - - +
76A LYS* 1.3 73.4 - - - +
78A ALA* 1.3 66.9 + - - +
80A ASN* 3.2 9.3 + - + +
81A LEU* 2.8 42.8 + - + +
503A CA 2.5 30.2 - - - -
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 4.2 14.1 - - + +
55A HIS* 3.9 19.7 - - + +
56A ASN* 3.8 26.7 - - - +
74A SER 3.0 14.0 + - - +
75A LEU* 3.4 10.8 - - - +
77A GLU* 1.3 77.1 - - - +
79A GLU* 1.3 62.2 + - - +
81A LEU* 4.0 2.8 - - - +
82A MET* 3.1 23.9 + - - +
97A THR* 4.1 6.5 - - + +
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU 3.1 11.9 + - - +
76A LYS* 3.6 8.6 - - - +
77A GLU 3.2 0.2 - - - -
78A ALA* 1.3 75.1 - - - +
80A ASN* 1.3 67.4 + - - +
82A MET* 3.3 15.0 + - - +
83A GLN* 3.4 19.9 + - - +
94A SER* 4.7 8.1 + - - +
97A THR* 3.7 14.8 - - + +
98A TRP* 2.8 36.4 + - - -
101A PHE* 3.7 16.8 - - + -
117A TYR* 4.5 6.4 + - - -
120A LYS* 6.0 0.2 - - - -
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LYS* 2.9 27.1 + - - +
77A GLU* 3.7 8.6 - - + +
79A GLU* 1.3 79.5 - - - +
81A LEU* 1.3 64.5 + - + +
83A GLN* 3.4 8.0 + - - +
84A GLU* 3.0 37.4 + - + +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A SER* 3.9 15.5 - - - +
52A VAL* 6.2 0.9 - - + -
55A HIS* 3.2 41.3 - - + +
77A GLU* 2.8 35.8 + - + +
78A ALA* 4.1 2.7 - - - +
80A ASN* 1.3 73.0 - - + +
82A MET* 1.3 65.9 + - - +
84A GLU* 4.5 6.3 - - + +
85A GLU* 3.2 51.4 + - + +
86A HIS* 4.1 2.2 + - - -
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TYR* 4.3 14.6 - - - -
52A VAL* 3.5 31.6 - - + +
78A ALA 3.1 19.5 + - - +
79A GLU* 3.5 9.4 - - - +
80A ASN 3.3 0.2 - - - -
81A LEU* 1.3 76.5 - - - +
83A GLN* 1.3 62.5 + - + +
86A HIS* 3.2 31.0 + - - +
89A GLN 4.8 9.2 - - - +
91A ASN* 3.7 25.4 - - + +
93A ARG* 3.6 12.8 - - + -
94A SER* 3.5 44.6 - - - +
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Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLU* 3.4 12.9 + - - +
80A ASN* 3.4 11.5 + - - +
81A LEU 3.2 0.4 - - - -
82A MET* 1.3 78.6 - - + +
84A GLU* 1.3 69.5 + - + +
85A GLU 3.0 3.2 + - - -
86A HIS 3.1 4.9 + - - -
87A ASP 3.5 0.2 + - - -
88A ASN* 2.9 64.2 + - - +
89A GLN 5.0 3.8 - - - +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASN* 3.0 36.2 + - + +
81A LEU* 3.5 8.0 + - + +
83A GLN* 1.3 78.1 - - + +
85A GLU* 1.3 65.0 + - + +
86A HIS 3.8 0.2 + - - -
87A ASP* 4.7 2.6 + - - -
88A ASN* 5.0 10.6 + - - +
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS 5.3 1.7 - - - +
51A SER* 4.9 7.8 + - - -
81A LEU* 3.2 37.7 + - + +
83A GLN 3.1 0.4 - - - -
84A GLU* 1.3 84.8 - - + +
86A HIS* 1.3 82.3 + - + +
87A ASP* 3.9 1.3 - - - -
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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