Contacts of the helix formed by residues 63 - 77 (chain A) in PDB entry 1M1B
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLU 3.7 2.3 + - - -
62A ALA* 1.3 75.9 - - - +
64A TRP* 1.3 68.9 + - - +
65A THR* 3.2 16.4 + - - -
66A GLN* 2.8 35.0 + - - +
67A VAL* 3.0 19.5 + - - +
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Residues in contact with TRP 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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62A ALA 3.9 0.4 + - - -
63A SER* 1.3 75.9 - - - +
65A THR* 1.3 80.2 + - + +
67A VAL* 3.0 11.9 + - - +
68A VAL* 2.8 41.3 + - + +
90A TYR* 3.6 46.2 - + + -
95A ASN* 5.4 11.2 + - + +
98A ARG* 3.9 36.1 - - + -
99A LEU* 3.6 32.5 - - + -
102A LYS* 3.7 33.9 - - + -
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Residues in contact with THR 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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63A SER* 3.2 14.4 + - - -
64A TRP* 1.3 113.1 - - + +
66A GLN* 1.3 62.8 + - - +
68A VAL* 3.7 6.3 - - - +
69A GLU* 2.8 28.8 + - - +
69B GLU* 5.3 9.3 + - - +
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Residues in contact with GLN 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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54A LEU* 5.5 4.7 - - + -
61A GLU 4.8 0.3 - - - +
62A ALA* 3.4 15.3 - - + +
63A SER* 2.8 43.9 + - - +
65A THR* 1.3 78.5 + - - +
67A VAL* 1.3 66.9 + - - +
69A GLU* 3.3 9.2 + - - +
70A VAL* 3.1 28.6 + - - +
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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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47A GLY* 6.5 1.1 - - - -
50A VAL* 4.6 16.4 - - + -
62A ALA* 4.6 14.8 - - + +
63A SER 3.0 18.8 + - - +
64A TRP* 3.0 10.3 + - - +
66A GLN* 1.3 78.4 - - - +
68A VAL* 1.3 63.5 + - + +
70A VAL* 3.3 5.1 + - - +
71A LEU* 3.0 27.6 + - + +
84A LEU* 3.9 26.0 - - + -
85A ASP 5.4 0.9 - - - +
87A ASP* 6.1 0.4 - - - +
90A TYR* 3.7 29.6 - - + +
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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 TRP* 2.8 32.0 + - + +
65A THR* 3.8 7.0 - - - +
66A GLN 3.2 0.2 - - - -
67A VAL* 1.3 76.6 - - + +
69A GLU* 1.3 59.8 + - - +
71A LEU* 3.2 7.3 + - + +
72A GLU* 2.7 27.5 + - - +
84A LEU* 5.5 0.9 - - + -
99A LEU* 3.6 30.1 - - + -
102A LYS* 4.4 13.7 - - + +
103A LEU* 4.6 14.4 - - + -
106A ARG* 4.2 31.2 - - + +
108A VAL* 6.2 0.2 - - + -
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Residues in contact with GLU 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 THR 2.8 20.0 + - - +
66A GLN* 3.7 10.4 - - - +
68A VAL* 1.3 76.5 - - - +
70A VAL* 1.3 67.9 + - + +
72A GLU* 2.8 36.0 + - - +
73A PHE* 3.2 27.1 + - + -
65B THR* 5.5 8.1 - - - +
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Residues in contact with VAL 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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27A HIS 3.9 21.5 - - - +
28A ASN* 4.7 2.5 - - - -
29A GLY 5.0 0.5 + - - -
50A VAL* 4.1 16.4 - - + -
53A GLN* 3.9 18.6 - - - +
54A LEU* 4.6 14.6 - - + -
66A GLN 3.1 18.4 + - - +
67A VAL 3.4 7.9 - - - +
69A GLU* 1.3 78.6 - - + +
71A LEU* 1.3 75.1 + - + +
73A PHE* 3.2 18.6 + - - +
74A MET* 3.3 17.1 + - + +
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Residues in contact with LEU 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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45A GLY* 4.7 2.7 - - - -
50A VAL* 4.1 12.1 - - + -
67A VAL* 3.0 18.8 + - + +
68A VAL* 3.5 11.4 - - + +
70A VAL* 1.3 89.7 - - + +
72A GLU* 1.3 60.4 + - - +
74A MET* 3.3 22.8 - - + +
75A SER* 2.9 29.8 + - - -
82A ILE* 3.6 33.9 - - + +
84A LEU* 3.5 39.0 - - + -
103A LEU* 5.4 1.3 - - + -
108A VAL* 4.6 16.0 - - + +
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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 2.7 15.7 + - - +
69A GLU* 3.1 28.2 - - - +
71A LEU* 1.3 73.6 - - - +
73A PHE* 1.3 69.1 + - + +
75A SER* 3.1 4.5 + - - -
76A ASP* 3.0 30.7 + - - +
106A ARG* 3.7 30.6 + - + -
102B LYS* 2.6 36.5 + - - +
106B ARG* 2.9 32.9 + - - +
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Residues in contact with PHE 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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29A GLY* 3.9 13.1 - - - +
69A GLU* 3.2 33.4 + - + -
70A VAL* 3.2 10.8 + - - +
72A GLU* 1.3 84.8 - - + +
74A MET* 1.3 59.6 + - - +
76A ASP* 3.7 9.6 + - + +
77A ALA* 3.2 24.4 + - - +
98B ARG* 3.5 28.7 - - - -
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ALA* 3.9 21.3 - - + +
27A HIS* 3.8 7.0 - - - -
28A ASN* 3.3 41.7 - - - +
29A GLY* 3.5 6.5 - - - +
32A ALA* 3.8 6.0 - - + +
43A ILE* 4.1 22.2 - - + -
45A GLY* 4.5 3.6 - - - -
50A VAL* 5.0 1.1 - - - -
70A VAL* 3.3 11.0 + - - +
71A LEU* 3.2 43.7 + - + +
72A GLU 3.1 0.2 - - - -
73A PHE* 1.3 76.4 - - - +
75A SER* 1.3 57.2 + - - +
77A ALA 3.4 7.3 + - - -
78A SER* 2.6 28.8 + - - -
82A ILE* 3.6 9.0 - - + -
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LYS* 2.9 34.4 + - - +
71A LEU 2.9 15.9 + - - -
72A GLU* 3.1 4.7 + - - -
74A MET* 1.3 73.4 - - - +
76A ASP* 1.3 67.6 + - - +
78A SER* 2.9 11.7 + - - +
82A ILE* 3.5 14.5 - - - +
106A ARG 2.6 29.8 + - - -
107A GLY* 3.4 11.4 - - - -
108A VAL* 4.6 3.8 - - - -
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Residues in contact with ASP 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 GLU* 3.0 21.4 + - - +
73A PHE* 3.9 9.9 - - + +
75A SER* 1.3 79.7 - - - +
77A ALA* 1.3 58.7 + - + +
78A SER 3.5 3.5 + - - +
106A ARG 4.5 4.5 - - - +
98B ARG* 4.2 11.3 + - - +
101B ARG* 4.2 23.2 + - - +
102B LYS* 2.6 34.5 + - - -
105B ASP* 5.3 3.8 - - - +
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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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29A GLY* 3.8 22.2 - - - +
33A ARG* 3.5 36.8 - - + +
36A GLN* 4.4 0.5 - - - +
73A PHE 3.2 16.7 + - - +
74A MET 3.4 3.1 + - - +
75A SER 3.1 1.0 - - - -
76A ASP* 1.3 79.4 - - - +
78A SER* 1.3 59.3 + - - +
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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