Contacts of the helix formed by residues 62 - 80 (chain A) in PDB entry 2CRU
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 LYS 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 2.8 29.8 + - + +
59A ALA 3.5 2.9 - - - -
61A VAL* 1.3 97.5 - - + +
63A PRO* 1.3 64.9 - - - +
64A GLU 3.4 2.7 - - - +
65A LYS* 3.8 28.0 - - + +
66A THR* 3.0 25.8 + - - -
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Residues in contact with PRO 63 (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* 3.0 24.9 - - + +
60A LEU 3.7 4.9 - - - +
61A VAL 3.4 9.0 - - - +
62A LYS* 1.3 87.7 - - - +
64A GLU* 1.3 73.7 + - + +
66A THR* 4.3 0.5 - - - -
67A LYS* 3.0 31.6 + - - +
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Residues in contact with GLU 64 (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 PRO* 1.3 83.7 - - + +
65A LYS* 1.3 68.7 + - - +
67A LYS* 3.1 25.0 - - - +
68A ALA* 3.3 7.1 + - - +
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 4.7 4.7 - - + -
62A LYS* 3.8 29.9 + - + -
63A PRO 3.4 0.2 - - - -
64A GLU* 1.3 81.7 - - - +
66A THR* 1.3 65.8 + - - +
68A ALA* 3.0 13.9 + - - +
69A VAL* 2.9 29.3 + - - +
95A LEU* 2.5 47.1 + - + +
98A VAL* 3.2 10.7 - - - +
99A SER* 4.9 7.3 - - - +
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Residues in contact with THR 66 (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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55A LEU* 3.0 46.4 - - + +
58A LEU* 3.0 23.0 - - + +
59A ALA* 3.2 25.9 + - + -
62A LYS 3.0 17.5 + - - -
63A PRO 4.3 0.2 - - - -
65A LYS* 1.3 78.9 - - - +
67A LYS* 1.3 66.0 + - - +
69A VAL* 2.8 22.9 + - - +
70A GLU* 3.0 13.1 + - + +
95A LEU* 4.4 1.1 - - - -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 5.4 6.7 + - - +
59A ALA* 5.9 0.2 - - - +
63A PRO 3.0 22.5 + - - +
64A GLU* 3.1 16.2 - - - +
65A LYS 3.0 0.4 + - - -
66A THR* 1.3 74.5 - - - +
68A ALA* 1.3 73.0 + - - +
70A GLU* 2.8 28.6 + - + +
71A ASN* 3.4 7.3 + - + +
103A GLU* 5.9 0.8 + - - -
105A THR* 5.3 11.9 - - - +
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Residues in contact with ALA 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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64A GLU 3.3 5.2 + - - +
65A LYS* 3.0 13.0 + - - +
67A LYS* 1.3 89.0 - - + +
69A VAL* 1.3 62.2 + - - +
71A ASN* 3.3 8.8 + - - +
72A TYR* 3.2 18.5 + - - +
98A VAL* 4.1 15.7 - - + -
103A GLU* 3.9 22.9 - - - +
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Residues in contact with VAL 69 (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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55A LEU* 4.4 15.0 - - + -
65A LYS* 2.9 45.1 - - - +
66A THR* 2.8 10.4 + - - +
68A ALA* 1.3 74.0 - - - +
70A GLU* 1.3 63.7 + - - +
72A TYR* 3.0 18.7 + - - +
73A LEU* 3.1 20.9 + - + +
91A LEU* 5.1 2.5 - - + -
94A ILE* 3.8 29.8 - - + -
95A LEU* 3.5 17.7 - - + +
98A VAL* 3.6 7.9 - - + -
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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
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39A ARG* 4.4 12.5 + - - +
43A LEU* 3.1 52.9 - - + +
47A LEU* 3.8 4.3 - - - +
52A ARG* 5.2 4.0 + - - -
55A LEU* 2.9 34.4 - - + +
66A THR* 3.0 17.1 + - + +
67A LYS* 2.8 15.8 + - + +
69A VAL* 1.3 78.6 - - - +
71A ASN* 1.3 61.8 + - - +
73A LEU* 4.3 1.8 - - - +
74A ILE* 3.3 20.1 + - - +
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Residues in contact with ASN 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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39A ARG* 5.0 5.3 - - - +
67A LYS* 3.4 7.6 + - + +
68A ALA* 3.3 12.0 + - - +
69A VAL 3.2 0.6 - - - -
70A GLU* 1.3 76.5 - - - +
72A TYR* 1.3 66.1 + - - +
74A ILE* 3.1 18.5 + - + +
75A GLN* 2.9 37.6 + - - +
103A GLU* 4.2 17.5 + - - +
104A LYS 5.6 1.2 + - - -
106A THR* 4.8 12.7 + - - -
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Residues in contact with TYR 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 ALA 3.2 8.8 + - - +
69A VAL* 3.0 13.6 + - - +
71A ASN* 1.3 79.1 - - - +
73A LEU* 1.3 56.1 + - - +
75A GLN* 2.8 47.8 - - - +
76A MET* 2.9 52.8 + - + +
81A GLN* 3.9 9.0 + - - -
94A ILE* 3.2 37.0 - - + +
97A LYS* 3.9 28.8 + - + -
98A VAL* 4.5 21.1 - - + -
103A GLU* 4.7 4.7 + - - +
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Residues in contact with LEU 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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43A LEU* 3.8 11.7 - - + -
46A VAL* 4.4 9.8 - - + +
47A LEU* 3.0 46.4 - - + -
55A LEU* 5.2 1.3 - - + -
69A VAL* 3.1 17.4 + - + +
70A GLU* 3.7 9.4 - - - +
72A TYR* 1.3 76.1 - - - +
74A ILE* 1.3 64.3 + - - +
76A MET* 3.3 25.5 + - + -
77A ALA* 3.0 18.9 + - - +
82A LEU* 3.1 19.4 - - + +
86A VAL* 5.2 2.2 - - + -
91A LEU* 4.0 10.1 - - + -
94A ILE* 4.1 23.6 - - + -
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Residues in contact with ILE 74 (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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39A ARG* 3.7 39.9 - - + +
42A ILE* 4.2 30.4 - - + +
43A LEU* 3.9 19.7 - - + -
70A GLU 3.3 16.1 + - - +
71A ASN* 3.1 20.5 + - - +
73A LEU* 1.3 76.9 - - - +
75A GLN* 1.3 66.7 + - - +
77A ALA* 3.0 19.4 + - - +
78A ARG* 3.4 18.3 + - + +
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Residues in contact with GLN 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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71A ASN* 2.9 29.2 + - - +
72A TYR* 2.8 51.9 - - - +
74A ILE* 1.3 78.1 - - - +
76A MET* 1.3 61.9 - - - +
78A ARG* 3.5 9.0 + - - +
79A TYR* 3.0 44.7 + - + -
81A GLN* 4.9 5.7 - - - +
103A GLU* 4.9 9.1 + - - +
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Residues in contact with MET 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 TYR* 2.9 68.4 + - + +
73A LEU* 3.4 25.1 - - + +
75A GLN* 1.3 78.2 - - + +
77A ALA* 1.3 61.5 + - - +
79A TYR* 3.7 0.5 - - - +
80A GLY 3.0 19.8 + - - -
81A GLN* 3.1 47.0 + - + +
82A LEU* 3.5 33.6 + - + -
94A ILE* 4.9 8.3 - - + -
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Residues in contact with ALA 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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42A ILE* 4.1 13.9 - - + -
45A GLN* 5.0 3.4 - - - +
46A VAL* 4.0 21.8 - - + -
73A LEU 3.0 10.4 + - - +
74A ILE 3.0 11.7 + - - +
76A MET* 1.3 76.1 - - - +
78A ARG* 1.3 70.0 + - + +
80A GLY* 3.2 10.4 + - - -
82A LEU* 3.6 10.7 - - - +
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Residues in contact with ARG 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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38A MET* 5.8 6.1 - - - +
42A ILE* 6.2 3.8 - - + -
74A ILE* 3.4 20.6 + - + +
75A GLN* 3.9 10.1 - - - +
77A ALA* 1.3 76.3 - - + +
79A TYR* 1.3 73.5 + - + +
80A GLY* 4.3 0.2 - - - -
108A VAL* 6.0 4.2 - - - +
112A ARG* 6.2 0.6 - - - +
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Residues in contact with TYR 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 GLN* 3.0 38.2 + - + +
76A MET 3.7 3.4 - - - +
78A ARG* 1.3 89.4 - - + +
80A GLY* 1.3 59.3 + - - +
81A GLN* 3.9 22.7 - - + +
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Residues in contact with GLY 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 MET 3.0 6.1 + - - -
77A ALA 3.2 9.7 + - - -
79A TYR* 1.3 77.4 - - - +
81A GLN* 1.3 65.6 + - - +
82A LEU 3.6 5.1 - - - +
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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