Contacts of the helix formed by residues 58 - 74 (chain A) in PDB entry 2I65
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 ARG 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A LYS* 1.3 116.7 - - + +
59A PHE* 1.3 65.0 + - - +
60A PRO* 3.3 4.7 - - - -
61A GLU* 3.2 32.4 + - + +
62A THR* 2.8 27.2 + - - +
170A TYR* 4.4 6.0 - - - -
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Residues in contact with PHE 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 THR* 3.4 19.7 - - + -
56A THR* 3.1 21.6 + - - +
57A LYS 4.1 1.1 - - - -
58A ARG* 1.3 75.6 - - - +
60A PRO* 1.4 65.3 - - + +
62A THR* 3.2 5.1 + - - -
63A VAL* 2.9 49.6 + - + +
86A TRP* 3.5 30.7 - + - -
89A PHE* 3.9 11.9 - + - -
93A PHE* 3.9 10.1 - + - -
154A ALA* 5.7 0.2 - - - -
157A LEU* 3.7 22.4 - - + -
158A THR 3.9 10.5 - - - -
159A TRP* 3.5 46.0 - + + -
168A ILE* 4.5 5.8 - - + -
170A TYR* 4.3 1.3 - - + -
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Residues in contact with PRO 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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58A ARG 3.5 4.3 - - - -
59A PHE* 1.4 93.2 - - + +
61A GLU* 1.3 71.5 + - + +
63A VAL* 3.4 2.1 + - - +
64A LEU* 3.0 26.9 + - - +
86A TRP* 3.4 42.9 - - + +
168A ILE* 3.8 9.6 - - + -
170A TYR* 3.3 25.1 - - - +
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Residues in contact with GLU 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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58A ARG* 3.2 33.8 + - + +
60A PRO* 1.3 96.3 - - + +
62A THR* 1.3 53.6 + - - +
64A LEU* 3.3 8.2 + - - +
65A ALA* 2.8 38.9 + - - +
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Residues in contact with THR 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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56A THR* 5.8 0.5 - - - +
57A LYS 4.2 3.9 + - - -
58A ARG* 2.8 30.2 + - - +
59A PHE* 3.5 7.4 - - - -
61A GLU* 1.3 73.9 - - - +
63A VAL* 1.3 60.2 + - - +
65A ALA* 3.8 4.3 - - - +
66A ARG* 2.8 62.9 + - + +
157A LEU* 3.9 23.3 - - + +
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Residues in contact with VAL 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 PHE* 2.9 52.6 + - + +
60A PRO 3.9 3.1 - - - +
62A THR* 1.3 75.4 - - - +
64A LEU* 1.3 58.3 + - - +
66A ARG* 3.3 4.2 + - - -
67A CYS* 2.8 30.3 + - + +
85A VAL* 5.3 1.1 - - + -
86A TRP* 3.9 28.5 - - + -
89A PHE* 4.0 19.1 - - + -
153A LEU* 3.5 33.5 - - + +
157A LEU* 4.2 1.3 - - + -
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Residues in contact with LEU 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 PRO 3.0 15.8 + - - +
61A GLU* 3.5 8.3 - - - +
63A VAL* 1.3 77.0 - - - +
65A ALA* 1.3 56.4 + - - +
67A CYS* 3.2 6.6 + - - +
68A VAL* 2.9 38.6 + - + +
82A CYS* 3.7 19.1 - - + +
83A GLN* 4.1 24.0 - - - +
86A TRP* 3.4 38.1 - - + -
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Residues in contact with ALA 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 GLU 2.8 22.1 + - - +
62A THR* 3.9 4.5 - - - +
64A LEU* 1.3 74.0 - - - +
66A ARG* 1.3 57.9 + - + +
68A VAL* 3.8 7.8 - - - +
69A LYS* 2.9 32.1 + - - +
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR* 2.8 39.0 + - + +
63A VAL 3.6 3.6 - - - +
65A ALA* 1.3 74.1 - - + +
67A CYS* 1.3 60.4 + - - +
69A LYS* 3.4 3.2 + - - +
70A TYR* 2.8 32.4 + - - +
152A TYR* 3.2 46.0 + - + +
153A LEU* 3.1 33.4 + - + -
155A ASP* 2.8 33.1 + - - +
156A ASP* 4.9 4.9 + - - +
157A LEU* 3.6 15.1 - - - +
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Residues in contact with CYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 2.8 18.1 + - + +
64A LEU* 3.4 6.3 - - - +
66A ARG* 1.3 77.0 - - - +
68A VAL* 1.3 55.5 + - - +
70A TYR* 3.2 1.4 + - - +
71A THR* 2.8 38.4 + - - +
80A VAL* 4.0 14.6 - - - -
82A CYS* 2.1 51.6 - - + +
85A VAL* 4.2 12.6 - - + -
149A LEU* 4.2 10.8 - - - -
153A LEU* 3.3 14.5 - - + +
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Residues in contact with VAL 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 LEU* 2.9 26.3 + - + +
65A ALA* 3.8 7.6 - - - +
67A CYS* 1.3 75.4 - - - +
69A LYS* 1.3 63.2 + - - +
71A THR* 3.2 7.5 + - - -
72A GLU* 3.0 52.1 + - + +
82A CYS* 3.4 15.5 - - + -
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Residues in contact with LYS 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 ALA* 2.9 20.2 + - - +
66A ARG* 3.7 5.6 - - - +
68A VAL* 1.3 75.3 - - - +
70A TYR* 1.3 65.6 + - - +
72A GLU* 3.2 14.2 + - - +
73A ILE* 3.1 40.7 + - + +
152A TYR* 3.3 24.1 + - + +
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Residues in contact with TYR 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 ARG 2.8 21.5 + - - +
67A CYS 3.7 3.1 - - - +
69A LYS* 1.3 73.4 - - - +
71A THR* 1.3 58.9 + - - +
73A ILE* 3.2 2.6 + - - -
74A HIS* 2.8 79.0 + + + +
77A MET* 3.8 19.5 - - + -
115A GLN* 2.8 19.2 + - - -
143A PHE* 4.8 0.7 - - - -
147A ASP* 2.6 31.8 + - - -
148A THR* 3.3 9.7 - - - -
149A LEU* 3.4 37.5 - - + -
152A TYR* 3.8 31.6 - + + -
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Residues in contact with THR 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 CYS* 2.8 27.4 + - - +
68A VAL* 3.2 11.8 + - - +
70A TYR* 1.3 74.3 - - - +
72A GLU* 1.3 60.9 + - - +
74A HIS 3.5 14.7 - - - +
77A MET* 3.3 31.0 - - + +
78A ARG* 3.9 18.7 - - - +
80A VAL* 3.8 29.8 + - + -
82A CYS* 3.8 8.1 - - - -
149A LEU* 4.4 7.2 - - + -
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Residues in contact with GLU 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 VAL* 3.0 42.2 + - + +
69A LYS* 3.6 12.5 - - - +
70A TYR 3.2 0.2 - - - -
71A THR* 1.3 80.5 - - - +
73A ILE* 1.3 69.5 + - + +
74A HIS 5.1 0.5 - - - -
75A PRO* 5.3 1.0 - - - +
78A ARG* 5.8 1.4 - - - +
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Residues in contact with ILE 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 LYS* 3.1 31.7 + - + +
70A TYR* 4.7 0.7 - - - -
72A GLU* 1.3 87.9 - - + +
74A HIS* 1.3 82.4 + - + +
75A PRO* 3.3 12.5 - - - +
140A ARG* 5.2 9.2 - - - +
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Residues in contact with HIS 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 TYR* 2.8 70.6 + + + +
71A THR 3.5 14.0 - - - +
72A GLU 5.0 0.2 - - - -
73A ILE* 1.3 94.4 - - + +
75A PRO* 1.3 70.5 - - + +
76A GLU* 3.2 23.3 - - - +
77A MET* 3.0 12.6 + - + +
140A ARG* 5.1 11.2 + - - -
143A PHE* 5.1 8.7 - + - -
147A ASP* 4.3 6.2 + - - +
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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