Contacts of the helix formed by residues 62 - 81 (chain A) in PDB entry 2PA2
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 SER 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A SER* 1.3 73.7 - - - +
63A GLU* 1.3 65.4 + - - +
65A LEU* 4.0 7.0 - - - -
66A GLU* 3.0 29.5 + - - +
94A PHE* 3.5 24.3 - - - -
124A GLY* 4.4 4.2 - - - -
125A THR* 3.1 43.6 + - - +
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Residues in contact with GLU 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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61A SER* 3.0 12.6 - - - +
62A SER* 1.3 91.9 + - - +
64A ALA* 1.3 59.4 + - - +
66A GLU* 4.0 3.6 - - - +
67A ALA* 2.9 30.0 + - - +
124A GLY* 4.6 11.6 - - - -
125A THR 4.4 2.4 - - - +
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Residues in contact with ALA 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 LEU* 5.2 3.4 - - + -
61A SER* 3.1 26.2 + - - +
63A GLU* 1.3 76.1 - - - +
65A LEU* 1.3 58.5 + - - +
67A ALA* 3.3 6.8 + - - +
68A ALA* 2.9 25.1 + - - +
158A LYS* 3.5 23.1 - - - +
159A PHE* 3.3 18.7 - - + -
160A PRO* 5.5 2.9 - - + -
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.0 19.7 - - + +
61A SER 3.1 20.5 + - - +
62A SER* 4.0 7.0 - - - +
64A ALA* 1.3 74.9 - - - +
66A GLU* 1.3 64.2 + - - +
68A ALA* 3.7 2.4 + - - +
69A ARG* 3.1 22.7 + - - +
89A VAL* 4.0 24.0 - - + +
91A LEU* 4.0 15.7 - - + -
93A PRO 5.1 2.7 - - - +
94A PHE* 4.1 19.7 - - + -
127A ALA* 4.0 20.0 - - + -
135A ILE* 3.9 17.5 - - + -
159A PHE* 3.4 26.5 - - + -
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Residues in contact with GLU 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 SER 3.0 20.6 + - - +
63A GLU* 4.0 3.6 - - - +
65A LEU* 1.3 74.0 - - - +
67A ALA* 1.3 68.6 + - - +
69A ARG* 2.6 40.8 + - - +
70A ILE* 2.9 46.0 + - + +
94A PHE* 3.0 27.5 - - + -
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Residues in contact with ALA 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 GLU 2.9 19.5 + - - +
64A ALA* 3.5 7.2 - - - +
66A GLU* 1.3 75.1 - - - +
68A ALA* 1.3 63.2 + - - +
70A ILE* 2.9 12.9 + - - +
71A CYS* 2.9 22.3 + - - +
158A LYS* 3.9 25.3 - - + -
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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 ALA 2.9 8.3 + - - +
65A LEU 3.8 1.1 - - - +
67A ALA* 1.3 76.9 - - - +
69A ARG* 1.3 56.8 + - - +
71A CYS* 3.4 0.8 + - - +
72A ALA* 3.0 26.7 + - - +
136A MET* 3.7 9.9 - - + -
155A ALA* 3.5 22.4 - - + +
158A LYS* 3.5 12.4 - - + +
159A PHE* 3.2 42.4 - - + -
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Residues in contact with ARG 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 LEU 3.1 14.6 + - - +
66A GLU* 2.6 41.5 + - - +
68A ALA* 1.3 72.6 - - - +
70A ILE* 1.3 76.3 + - - +
72A ALA* 3.6 1.5 + - - +
73A ASN* 2.9 54.6 + - - +
87A ILE* 4.2 25.4 - - + +
88A ARG* 5.6 1.8 - - - +
89A VAL* 4.0 27.8 - - + +
94A PHE* 4.5 5.8 - - - -
136A MET* 4.3 9.3 - - - -
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Residues in contact with ILE 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 GLU* 2.9 43.5 + - + +
67A ALA* 3.2 9.4 - - - +
69A ARG* 1.3 88.8 - - - +
71A CYS* 1.3 59.4 + - - +
73A ASN* 3.1 4.7 + - + +
74A LYS* 2.8 63.5 + - + +
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Residues in contact with CYS 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 ALA 2.9 10.4 + - - +
68A ALA 3.6 8.5 - - - +
70A ILE* 1.3 81.1 - - - +
72A ALA* 1.3 62.7 + - - +
74A LYS* 3.3 6.0 + - - +
75A TYR* 3.3 20.6 + - - +
154A ARG* 3.8 21.5 - - - -
155A ALA* 3.8 27.1 - - - -
158A LYS* 3.9 22.2 - - - -
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Residues in contact with ALA 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 3.0 16.5 + - - +
71A CYS* 1.3 77.7 - - - +
73A ASN* 1.3 62.6 + - - +
75A TYR* 3.5 0.3 + - - +
76A MET* 3.1 28.4 + - - +
87A ILE* 3.5 23.8 - - + -
136A MET* 4.2 6.7 - - - -
138A ILE* 4.6 3.4 - - + -
151A ALA* 3.9 26.3 - - + +
152A LEU* 5.0 0.9 - - + -
155A ALA* 3.9 13.0 - - + +
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Residues in contact with ASN 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 ARG* 2.9 38.3 + - - +
70A ILE* 3.1 6.8 + - + +
72A ALA* 1.3 77.2 - - - +
74A LYS* 1.3 70.4 + - + +
76A MET* 3.1 5.0 + - - +
77A VAL* 2.9 35.8 + - - +
82A LYS* 6.1 0.7 - - - -
85A PHE* 3.0 36.0 - - - -
87A ILE* 3.7 14.2 - - + +
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Residues in contact with LYS 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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70A ILE* 2.8 51.2 + - + +
71A CYS* 3.6 7.4 - - - +
73A ASN* 1.3 81.5 + - + +
75A TYR* 1.3 59.5 - - - +
77A VAL* 2.8 29.4 - - + +
78A LYS* 3.3 13.3 + - + +
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Residues in contact with TYR 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 CYS 3.3 13.2 + - - +
72A ALA 4.0 3.1 - - - +
74A LYS* 1.3 79.1 - - - +
76A MET* 1.3 53.5 + - - +
78A LYS* 3.6 18.0 - - + +
79A SER* 2.7 55.2 + - - -
147A HIS* 3.3 48.4 + - - -
150A GLU* 3.4 21.8 - - + +
151A ALA* 3.9 16.8 - - + -
154A ARG* 3.7 45.8 - - + +
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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 ALA 3.1 22.6 + - - +
73A ASN 3.1 0.6 + - - +
75A TYR* 1.3 75.6 - - - +
77A VAL* 1.3 58.4 + - - +
79A SER* 3.6 2.0 - - - -
80A CYS* 2.7 65.0 + - - +
81A GLY 3.5 0.5 + - - -
85A PHE* 3.5 52.1 - - + -
87A ILE* 5.3 0.4 - - + -
138A ILE* 3.9 22.7 - - + -
140A THR* 4.5 3.1 - - - -
147A HIS 3.9 14.1 - - - +
148A VAL* 4.2 13.0 - - + -
151A ALA* 3.7 22.9 - - + -
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Residues in contact with VAL 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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73A ASN* 2.9 26.8 + - - +
74A LYS* 2.8 33.9 - - + +
76A MET* 1.3 75.8 - - - +
78A LYS* 1.3 64.8 + - + +
81A GLY* 2.8 27.5 + - - -
82A LYS* 3.7 36.6 + - + +
85A PHE* 3.6 22.7 - - + -
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Residues in contact with LYS 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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74A LYS 3.4 16.8 - - - +
75A TYR* 3.6 22.0 - - + +
77A VAL* 1.3 82.9 - - + +
79A SER* 1.3 61.4 + - - +
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Residues in contact with SER 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 TYR* 2.7 35.1 + - - -
76A MET* 3.4 4.0 + - - -
78A LYS* 1.3 81.3 - - - +
80A CYS* 1.3 73.9 + - - +
81A GLY 3.8 0.2 - - - -
144A ASN* 4.6 1.6 - - - +
147A HIS* 3.5 42.8 + - - +
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Residues in contact with CYS 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* 2.7 43.2 + - + +
79A SER* 1.3 90.8 - - - +
81A GLY* 1.3 62.0 + - - +
84A GLY* 3.5 19.0 - - - +
85A PHE* 4.5 0.2 - - + -
144A ASN* 3.5 42.3 + - - +
147A HIS* 3.8 6.1 - - - -
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Residues in contact with GLY 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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76A MET 3.5 0.2 + - - -
77A VAL* 2.8 18.1 + - - -
78A LYS 4.8 0.2 - - - -
79A SER 3.8 0.2 - - - -
80A CYS* 1.3 79.7 - - - +
82A LYS* 1.3 53.6 + - - -
83A ASP 2.7 7.4 + - - -
84A GLY* 2.6 26.7 + - - -
85A PHE* 3.5 8.1 - - - -
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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