Contacts of the helix formed by residues 60 - 73 (chain A) in PDB entry 3MI9
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 PRO 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A VAL* 4.4 1.6 - - + -
51A LEU 3.9 20.9 - - - +
52A MET* 3.9 19.7 - - + -
54A ASN 5.3 5.4 - - - +
57A GLU* 5.4 1.3 - - + +
58A GLY 3.6 7.4 - - - +
59A PHE* 1.3 93.5 - - + +
61A ILE* 1.3 54.9 + - - +
62A THR* 2.8 27.1 - - + -
63A ALA* 2.7 32.0 + - + +
64A LEU* 2.9 12.8 + - - +
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Residues in contact with ILE 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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59A PHE 3.3 4.0 + - - -
60A PRO* 1.3 71.5 - - - +
62A THR* 1.3 63.5 + - - +
64A LEU* 3.7 12.9 - - + +
65A ARG* 2.9 48.8 + - + +
93B LYS* 3.7 39.8 - - + +
96B GLU* 4.5 13.0 - - - +
98B PRO* 4.0 28.7 - - + -
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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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60A PRO* 2.8 20.8 - - + -
61A ILE* 1.3 88.3 - - + +
63A ALA* 1.3 64.7 + - + +
65A ARG* 3.5 10.7 + - - +
66A GLU* 3.1 22.1 + - - +
169A GLY 2.8 29.9 + - - +
170A LEU* 4.4 8.5 - - - +
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Residues in contact with ALA 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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50A VAL* 4.0 19.5 - - + -
59A PHE* 3.5 21.8 - - + -
60A PRO* 2.7 21.0 + - + +
62A THR* 1.3 80.0 - - + +
64A LEU* 1.3 65.0 + - - +
66A GLU* 3.1 12.3 + - - +
67A ILE* 2.9 30.1 + - + +
101A LEU* 6.1 0.4 - - + -
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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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59A PHE* 3.5 28.5 - - + +
60A PRO 2.9 11.9 + - - +
61A ILE* 3.7 14.8 - - + +
63A ALA* 1.3 75.6 - - - +
65A ARG* 1.3 58.0 + - - +
67A ILE* 3.4 6.7 + - + +
68A LYS* 2.9 32.4 + - - +
90B LEU* 3.7 15.7 - - + -
93B LYS* 3.7 39.7 - - + +
94B VAL* 4.6 10.3 - - + -
141B LEU* 3.9 24.0 - - + -
148B LEU* 4.0 16.8 - - + +
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Residues in contact with ARG 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 ILE* 2.9 40.8 + - + +
62A THR* 3.7 9.3 - - - +
64A LEU* 1.3 78.0 - - - +
66A GLU* 1.3 57.5 + - - +
68A LYS* 3.8 5.2 - - - +
69A ILE* 2.9 41.4 + - + +
148A ARG* 3.5 11.5 - - - +
169A GLY 6.0 0.4 - - - +
171A ALA 3.7 20.9 - - - +
172A ARG* 3.8 20.6 - - - +
186A TPO 3.0 41.8 + - - -
96B GLU* 2.7 44.2 + - - +
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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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48A LYS* 2.7 36.7 + - - -
62A THR 3.1 10.2 + - - +
63A ALA* 3.1 13.9 + - - +
65A ARG* 1.3 80.0 - - - +
67A ILE* 1.3 52.5 + - - +
69A ILE* 3.6 3.1 - - - +
70A LEU* 2.7 54.5 + - + +
101A LEU* 3.6 20.1 - - + +
103A PHE* 4.0 3.8 - - - -
167A ASP* 4.9 0.2 - - - -
168A PHE* 3.4 33.1 + - + +
169A GLY* 3.3 18.8 + - - -
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Residues in contact with ILE 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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59A PHE* 3.9 27.4 - - + -
63A ALA* 2.9 22.0 + - + +
64A LEU* 3.7 7.0 - - + +
66A GLU* 1.3 75.7 - - - +
68A LYS* 1.3 58.7 + - - +
70A LEU* 3.2 7.7 + - - +
71A GLN* 2.9 56.4 + - + +
81A LEU* 4.8 1.8 - - + -
84A ILE* 3.4 37.2 - - + -
101A LEU* 4.2 22.2 - - + -
146B PHE* 3.9 13.5 - - + +
148B LEU* 3.9 11.2 - - + -
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Residues in contact with LYS 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 18.4 + - - +
65A ARG* 3.8 5.4 - - - +
67A ILE* 1.3 78.1 - - - +
69A ILE* 1.3 64.4 + - + +
71A GLN* 3.3 11.5 + - - +
72A LEU* 3.0 22.5 + - - +
94B VAL* 4.2 34.5 - - + +
95B GLU* 5.5 5.4 - - - -
148B LEU* 4.4 9.4 - - + -
149B THR* 3.2 48.0 + - - +
10C PRO* 6.3 1.6 - - - +
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Residues in contact with ILE 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 ARG* 2.9 26.7 + - + +
66A GLU* 3.8 4.5 - - - +
68A LYS* 1.3 79.1 - - + +
70A LEU* 1.3 57.6 + - - +
72A LEU* 3.0 6.5 + - - +
73A LEU* 2.9 54.9 + - + +
145A ILE* 3.8 25.8 - - + -
168A PHE* 3.9 14.4 - - + -
171A ALA* 3.6 37.9 - - + +
172A ARG* 3.7 15.9 - - - +
173A ALA* 4.5 1.8 - - + +
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Residues in contact with LEU 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* 2.7 49.9 + - + +
67A ILE 3.7 0.7 - - - +
69A ILE* 1.3 72.9 - - - +
71A GLN* 1.3 61.4 + - - +
73A LEU* 3.2 21.5 - - + +
74A LYS* 3.4 13.1 + - - -
78A VAL* 5.5 2.5 - - + -
79A VAL* 3.8 36.5 - - + +
81A LEU* 3.6 23.9 + - + +
101A LEU* 3.7 12.1 - - + -
103A PHE* 3.7 28.0 - - + -
168A PHE* 4.1 18.6 - - + +
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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 ILE* 2.9 40.6 + - + +
68A LYS* 3.7 9.3 - - - +
70A LEU* 1.3 77.2 - - - +
72A LEU* 1.3 61.4 + - - +
74A LYS* 3.9 18.2 - - - +
81A LEU* 4.3 10.3 - - + +
84A ILE* 4.7 5.1 - - - +
145B GLY 4.6 2.8 + - - -
146B PHE* 3.0 34.9 + - - +
147B GLU* 4.5 5.8 - - - +
148B LEU* 4.3 8.5 + - - +
149B THR* 5.3 3.2 + - - +
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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 LYS* 3.0 14.0 + - + +
69A ILE* 3.0 9.7 + - + +
71A GLN* 1.3 80.8 - - - +
73A LEU* 1.3 75.2 + - + +
74A LYS* 3.4 7.4 + - - +
139A TYR* 3.6 5.7 + - - -
143A ASN* 4.0 33.9 - - + +
145A ILE* 4.4 12.8 - - + -
149B THR* 6.1 2.7 - - + +
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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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69A ILE* 2.9 41.9 + - + +
70A LEU* 3.2 10.2 - - + +
72A LEU* 1.3 76.8 - - + +
74A LYS* 1.3 73.0 + - - +
75A HIS 4.1 0.8 + - - -
78A VAL* 4.1 17.9 - - + +
79A VAL 4.6 4.2 - - - +
139A TYR* 3.5 26.0 - - + -
140A ILE* 4.0 17.0 - - + -
143A ASN* 3.7 28.5 - - + -
145A ILE* 4.2 11.0 - - + -
168A PHE* 3.8 24.5 - - + -
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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