Contacts of the helix formed by residues 52 - 72 (chain A) in PDB entry 2Y1M
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A THR* 3.9 4.2 + - - -
51A VAL* 1.3 78.9 - - - +
53A LYS* 1.3 59.6 + - - +
54A LYS* 3.5 15.2 + - - +
55A MET* 2.8 38.2 + - - +
56A VAL 3.5 2.6 + - - -
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Residues in contact with LYS 53 (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 VAL 4.3 0.4 + - - -
52A ASP* 1.3 70.0 - - - +
54A LYS* 1.3 66.8 + - - +
55A MET 2.9 1.4 + - - -
56A VAL* 3.0 23.0 + - + -
57A GLU* 3.0 45.8 + - + +
60A TRP* 4.6 4.5 - - - -
96A ARG* 4.1 15.2 - - - +
99A LEU* 3.9 28.1 - - + +
106A MET* 5.5 19.5 - - + +
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Residues in contact with LYS 54 (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 ASP* 3.1 15.1 + - + +
53A LYS* 1.3 78.7 - - - +
55A MET* 1.3 59.5 + - - +
57A GLU* 3.5 16.0 + - - +
58A LYS* 3.5 12.3 + - - +
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Residues in contact with MET 55 (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 THR 5.0 5.2 - - - +
51A VAL* 4.2 25.8 - - + -
52A ASP* 2.8 23.8 + - - +
54A LYS* 1.3 74.7 - - - +
56A VAL* 1.3 63.7 + - - +
57A GLU 3.1 2.2 - - - -
58A LYS* 3.6 9.1 + - - +
59A CYS* 3.2 21.3 + - - +
119A MET* 3.5 39.7 - - + +
120A GLU* 4.4 7.9 - - + +
123A MET* 3.9 31.5 - - + +
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Residues in contact with VAL 56 (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 VAL* 5.0 6.7 - - + +
52A ASP 3.5 3.4 + - - +
53A LYS* 3.0 37.2 + - + +
55A MET* 1.3 79.6 - - - +
57A GLU* 1.3 74.0 + - - +
59A CYS* 3.4 1.4 + - - +
60A TRP* 3.2 53.6 + - + +
95A LEU* 4.9 2.5 - - + -
99A LEU* 4.2 17.7 - - + -
115A PHE* 5.6 2.2 - - + -
119A MET* 3.6 29.4 - - + -
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Residues in contact with GLU 57 (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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53A LYS* 3.0 57.8 + - + +
54A LYS* 3.5 10.8 - - - +
55A MET 3.1 0.2 - - - -
56A VAL* 1.3 75.9 - - - +
58A LYS* 1.3 66.0 + - - +
59A CYS 3.1 1.3 - - - -
60A TRP* 2.9 39.3 + - - +
61A LYS* 3.0 12.7 + - - +
96A ARG* 5.7 0.2 + - - -
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Residues in contact with LYS 58 (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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54A LYS 3.5 10.3 + - - +
55A MET* 4.0 12.5 - - - +
56A VAL 3.5 0.2 - - - -
57A GLU* 1.3 77.5 - - - +
59A CYS* 1.3 58.6 + - - +
60A TRP 3.0 5.4 + - - -
61A LYS* 3.0 24.8 + - + +
62A LEU* 3.0 26.6 + - + +
123A MET* 3.7 29.3 - - + -
127A LYS* 5.2 9.6 - - - +
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Residues in contact with CYS 59 (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 MET* 3.2 16.4 + - - +
56A VAL 3.4 8.3 - - - +
57A GLU 3.1 0.2 - - - -
58A LYS* 1.3 78.6 - - - +
60A TRP* 1.3 59.5 + - + +
62A LEU* 4.1 6.5 - - - +
63A MET* 3.0 29.3 + - - +
119A MET* 3.6 24.9 - - + -
122A LEU* 3.3 31.4 - - + -
123A MET* 3.9 35.6 - - + +
126A THR* 5.1 1.0 - - - +
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Residues in contact with TRP 60 (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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53A LYS* 4.6 0.4 - - - -
56A VAL* 3.2 27.3 + - + +
57A GLU* 2.9 39.3 + - - +
59A CYS* 1.3 85.5 - - + +
61A LYS* 1.3 65.2 + - - +
62A LEU 3.1 2.0 - - - -
63A MET* 3.4 19.8 + - - +
64A ASP* 3.1 21.5 + - - +
92A TYR* 3.8 28.0 - + + -
95A LEU* 3.6 34.4 - - + +
96A ARG* 2.9 44.0 - - + -
99A LEU* 3.6 27.1 - - + -
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Residues in contact with LYS 61 (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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57A GLU 3.0 10.4 + - - +
58A LYS* 3.0 17.9 + - + +
60A TRP* 1.3 76.4 - - - +
62A LEU* 1.3 65.0 + - + +
64A ASP* 3.3 8.3 + - - +
65A LYS* 3.1 19.9 + - - +
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Residues in contact with LEU 62 (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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58A LYS* 3.0 27.9 + - + +
59A CYS* 4.2 4.3 - - - +
61A LYS* 1.3 77.6 - - + +
63A MET* 1.3 66.4 + - - +
64A ASP 2.9 2.0 - - - -
65A LYS* 2.8 18.4 + - + +
66A VAL* 3.1 14.6 + - - +
123A MET* 4.0 28.3 - - + -
126A THR* 3.2 36.3 - - + +
127A LYS* 4.2 19.5 - - + -
130A ILE* 3.8 19.9 - - + +
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Residues in contact with MET 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 CYS 3.0 20.8 + - - +
60A TRP* 3.4 24.4 + - - +
62A LEU* 1.3 76.3 - - - +
64A ASP* 1.3 60.1 + - - +
66A VAL* 3.6 4.0 + - - +
67A VAL* 3.2 28.8 + - - +
88A LEU* 3.3 53.0 - - + +
91A THR* 3.8 17.0 - - + -
92A TYR* 3.8 17.7 - - + +
95A LEU* 4.7 1.8 - - - -
122A LEU* 3.6 25.1 - - + -
126A THR* 3.6 11.2 + - - +
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Residues in contact with ASP 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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60A TRP 3.1 12.9 + - - +
61A LYS* 3.5 12.3 - - - +
62A LEU 2.9 0.8 - - - -
63A MET* 1.3 75.6 - - - +
65A LYS* 1.3 66.6 + - - +
67A VAL* 3.2 8.7 + - - +
68A ARG* 3.0 69.7 + - - +
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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
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61A LYS* 3.1 12.4 + - + +
62A LEU* 2.8 10.0 + - + +
64A ASP* 1.3 78.8 - - - +
66A VAL* 1.3 56.1 + - - +
68A ARG* 3.6 11.1 + - + +
69A LEU* 3.1 53.6 + - + +
130A ILE* 4.0 34.1 - - + +
134A LYS* 6.2 0.4 - - - +
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Residues in contact with VAL 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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62A LEU 3.1 12.9 + - - +
63A MET* 4.0 7.2 - - - +
65A LYS* 1.3 74.3 - - - +
67A VAL* 1.3 62.0 + - - +
69A LEU* 3.9 7.1 - - - +
70A CYS* 2.9 41.1 + - - -
84A ILE* 3.9 4.7 - - + -
88A LEU* 3.9 20.4 - - + -
126A THR* 3.6 33.2 - - - +
129A THR* 3.5 27.8 - - + -
130A ILE* 3.8 9.9 - - + -
133A PHE* 5.3 0.4 - - + -
158A PHE* 5.3 1.6 - - + -
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Residues in contact with VAL 67 (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 MET* 3.2 19.5 + - + +
64A ASP* 3.2 10.3 + - - +
66A VAL* 1.3 77.3 - - - +
68A ARG* 1.3 67.6 + - - +
70A CYS* 3.2 1.6 + - - -
71A GLN* 2.9 45.1 + - - +
85A LEU* 3.6 20.9 - - + +
88A LEU* 3.7 27.6 - - + -
89A PRO* 4.3 15.7 - - + -
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Residues in contact with ARG 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 ASP* 3.0 49.6 + - - +
65A LYS* 3.7 12.6 - - + +
67A VAL* 1.3 76.9 - - - +
69A LEU* 1.3 65.6 + - + +
71A GLN* 3.0 35.5 + - - +
72A ASN* 3.5 5.4 + - - +
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Residues in contact with LEU 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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65A LYS* 3.1 44.2 + - + +
66A VAL* 3.9 6.1 - - + +
68A ARG* 1.3 79.2 - - + +
70A CYS* 1.3 58.9 + - - +
72A ASN* 3.5 12.2 + - - +
75A LEU* 3.1 16.3 - - - +
130A ILE* 4.1 22.9 - - + +
133A PHE* 3.4 50.2 - - + -
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Residues in contact with CYS 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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66A VAL* 2.9 41.1 + - - +
68A ARG 3.2 0.2 - - - -
69A LEU* 1.3 73.8 - - - +
71A GLN* 1.3 60.9 + - - +
72A ASN 3.2 3.8 + - - +
75A LEU* 3.4 12.2 - - - +
77A LEU* 3.6 26.8 + - + +
84A ILE* 3.9 21.5 - - + -
85A LEU* 3.7 23.6 - - + +
88A LEU* 5.6 0.2 - - - -
133A PHE* 4.0 17.9 - - - -
151A LEU* 4.3 6.7 - - - -
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Residues in contact with GLN 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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67A VAL* 2.9 28.3 + - - +
68A ARG* 3.0 31.1 + - - +
70A CYS* 1.3 75.8 - - - +
72A ASN* 1.3 69.1 + - - +
73A PRO* 3.1 7.2 - - - +
85A LEU* 3.9 22.9 - - + -
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Residues in contact with ASN 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 ARG 3.5 5.7 + - - +
69A LEU* 3.5 16.9 + - - +
70A CYS 3.2 1.3 - - - +
71A GLN* 1.3 79.0 - - - +
73A PRO* 1.3 88.9 - - - +
74A LYS* 3.0 31.3 + - - +
75A LEU* 3.1 24.0 + - + +
76A ALA 3.7 2.8 + - - -
77A LEU 5.3 0.2 + - - -
141A TYR* 3.8 27.1 + - - -
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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