Contacts of the helix formed by residues 57 - 75 (chain A) in PDB entry 1MF8
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 GLU 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A HIS* 5.5 1.2 - - - -
28A ARG* 3.4 29.3 - - + +
29A LEU 2.9 23.6 + - - +
30A THR* 4.5 16.7 - - - +
31A ALA 5.3 0.7 + - - -
56A LEU* 1.3 70.9 - - - +
58A GLU* 1.3 67.7 + - - +
59A SER* 3.3 11.7 + - - +
60A VAL* 2.7 31.7 + - + +
61A ALA 3.2 1.7 + - - -
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Residues in contact with GLU 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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28A ARG* 5.1 10.8 + - - +
56A LEU 3.2 5.1 + - - -
57A GLU* 1.3 69.6 - - - +
59A SER* 1.3 64.5 + - - +
61A ALA* 3.1 4.2 + - - +
62A LEU* 2.8 29.6 + - + +
170A TYR* 4.3 19.5 - - + +
171A SER* 2.5 36.3 + - - -
173A ARG* 3.9 19.0 + - - +
174A VAL* 3.6 21.6 - - + +
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 4.1 16.6 + - - +
58A GLU* 1.3 74.6 - - - +
60A VAL* 1.3 70.9 + - - +
62A LEU* 3.0 10.1 + - - +
63A ARG* 2.8 24.5 + - - +
173A ARG* 6.1 3.1 - - - +
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Residues in contact with VAL 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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29A LEU 3.4 19.3 - - - +
30A THR* 4.0 3.1 - - - +
31A ALA* 3.8 21.8 - - + +
34A VAL* 3.3 40.2 - - + -
35A PHE* 4.1 6.1 - - + -
56A LEU* 3.8 14.4 - - + -
57A GLU* 2.7 32.9 + - + +
59A SER* 1.3 74.9 + - - +
61A ALA* 1.3 60.9 + - - +
63A ARG* 3.2 19.1 + - - +
64A ILE* 3.3 10.4 + - - +
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Residues in contact with ALA 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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56A LEU* 4.3 7.8 - - + +
57A GLU 3.2 4.2 + - - +
58A GLU 3.1 9.9 + - - +
60A VAL* 1.3 78.9 - - - +
62A LEU* 1.3 58.6 + - - +
64A ILE* 3.0 6.9 + - - +
65A ILE* 2.8 37.9 + - + +
131A LEU* 3.4 29.6 - - + -
170A TYR* 4.3 19.7 - - + -
174A VAL* 5.1 4.7 - - + -
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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 GLU* 2.8 33.6 + - + +
59A SER* 3.4 12.3 - - - +
61A ALA* 1.3 73.0 - - - +
63A ARG* 1.3 57.6 + - - +
65A ILE* 3.9 4.9 - - + -
66A THR* 2.8 38.4 + - + +
173A ARG* 4.4 28.9 - - + +
174A VAL* 3.2 39.9 - - + +
177A ALA* 3.0 37.0 - - + -
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Residues in contact with ARG 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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31A ALA* 4.2 16.4 - - - +
35A PHE* 3.3 49.5 - - + +
39A GLY* 4.4 13.7 + - - -
59A SER 2.8 11.3 + - - +
60A VAL* 3.2 13.2 - - - +
61A ALA 3.0 0.2 - - - -
62A LEU* 1.3 75.8 - - - +
64A ILE* 1.3 55.3 + - - +
66A THR* 2.8 8.3 + - - -
67A GLU* 2.5 71.9 + - + +
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Residues in contact with ILE 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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34A VAL* 3.9 18.6 - - + -
35A PHE* 3.2 23.6 - - + -
41A PRO* 6.3 0.2 - - + -
46A LEU* 4.1 11.2 - - + -
56A LEU* 3.9 28.3 - - + -
60A VAL 3.3 7.2 + - - +
61A ALA* 3.0 7.6 + - - +
63A ARG* 1.3 78.4 - - - +
65A ILE* 1.3 62.9 + - + +
67A GLU 3.3 0.2 + - - -
68A GLY 3.1 21.1 + - - -
131A LEU* 3.5 28.5 - - + +
134A TRP* 3.6 17.3 - - + -
135A ALA* 3.7 15.5 - - + +
138A ILE* 3.5 11.4 - - + +
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Residues in contact with ILE 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 ALA* 2.8 27.4 + - + +
62A LEU* 3.9 8.5 - - - +
64A ILE* 1.3 79.0 - - + +
66A THR* 1.3 57.7 + - - +
69A ALA* 3.5 15.9 + - - +
127A ILE* 5.0 2.7 - - + -
130A VAL* 5.4 3.6 - - + -
131A LEU* 4.8 11.4 - - + -
134A TRP* 3.4 30.3 + - + +
174A VAL* 3.5 33.7 - - + +
177A ALA* 3.7 33.4 - - + +
178A CYS* 3.6 23.8 - - - +
181A ALA* 4.0 1.3 - - + +
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Residues in contact with THR 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* 2.8 31.2 + - + +
63A ARG* 2.8 21.5 + - - -
65A ILE* 1.3 78.6 - - + +
67A GLU* 1.3 69.2 + - - +
68A GLY 3.3 0.4 - - - -
69A ALA* 3.5 5.6 + - - +
70A SER* 3.4 19.4 + - - -
73A ARG* 5.9 0.3 + - - -
177A ALA* 4.8 7.6 - - + +
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Residues in contact with GLU 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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35A PHE* 3.6 13.7 - - - -
39A GLY 4.7 3.6 - - - +
63A ARG* 2.5 71.8 + - + +
64A ILE 3.3 0.2 + - - -
66A THR* 1.3 75.6 + - - +
68A GLY* 1.3 60.2 + - - +
70A SER* 2.4 29.8 + - - -
71A ILE* 3.4 8.3 - - + +
138A ILE* 3.3 33.3 - - + +
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Residues in contact with GLY 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 ILE 3.1 13.9 + - - -
67A GLU* 1.3 77.2 - - - +
69A ALA* 1.3 56.7 + - - +
70A SER 3.3 0.2 - - - -
71A ILE* 3.5 10.6 + - - +
72A LEU* 3.0 32.6 + - - +
134A TRP* 4.6 14.1 - - - -
137A LYS* 4.5 7.8 - - - +
138A ILE* 3.7 16.0 - - - +
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Residues in contact with ALA 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 ILE 3.5 19.5 + - - +
66A THR* 3.5 8.0 + - - +
67A GLU 3.3 0.8 - - - -
68A GLY* 1.3 74.5 - - - +
70A SER* 1.3 60.2 + - - +
71A ILE 3.3 0.2 - - - -
72A LEU* 3.3 11.9 - - - +
73A ARG* 2.8 39.8 + - - +
134A TRP* 4.5 0.6 - - - +
177A ALA 5.8 0.2 - - - +
181A ALA* 3.7 29.4 - - + +
184A CYS* 3.6 7.7 - - - -
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Residues in contact with SER 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 THR 3.4 8.5 + - - -
67A GLU* 2.4 29.4 + - - -
69A ALA* 1.3 79.3 - - - +
71A ILE* 1.3 60.8 + - - +
73A ARG* 3.3 22.0 + - - +
74A GLN* 2.7 49.0 + - - +
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Residues in contact with ILE 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 GLU* 3.4 16.4 - - + +
68A GLY* 3.5 9.4 - - - +
70A SER* 1.3 79.4 - - - +
72A LEU* 1.3 57.4 + - - +
74A GLN* 3.5 14.8 + - - +
75A GLU* 3.1 42.1 + - + +
137A LYS* 4.0 12.3 - - + +
138A ILE* 3.8 36.8 - - + +
141A PRO* 3.9 26.5 - - + -
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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 GLY 3.0 19.6 + - - +
69A ALA* 3.3 12.6 - - - +
70A SER 3.1 0.2 - - - -
71A ILE* 1.3 73.4 - - - +
73A ARG* 1.3 55.5 - - - +
74A GLN 3.1 2.2 - - - -
75A GLU* 3.2 21.3 + - - +
134A TRP* 3.9 19.5 - - + -
137A LYS* 4.4 13.5 - - + -
146A LEU* 4.4 10.5 - - + +
181A ALA 4.1 13.0 - - - +
184A CYS* 2.8 11.1 - - + +
185A LEU* 3.2 31.0 - - + -
186A PRO* 3.6 26.2 - - + -
217A ARG* 2.6 29.1 + - - -
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Residues in contact with ARG 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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66A THR 5.9 0.6 + - - -
69A ALA* 2.8 28.1 + - - +
70A SER* 3.8 30.1 + - - +
72A LEU* 1.3 73.7 - - - +
74A GLN* 1.3 61.5 + - + +
75A GLU 3.7 1.2 + - - +
180A ASP* 5.6 7.5 + - - +
184A CYS* 3.3 21.1 - - + +
217A ARG* 3.8 1.4 + - - -
218A PHE* 3.2 46.8 - - + -
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Residues in contact with GLN 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 SER* 2.7 37.1 + - - +
71A ILE* 3.5 14.6 - - - +
72A LEU 3.1 0.2 - - - -
73A ARG* 1.3 80.4 - - + +
75A GLU* 1.3 62.5 + - + +
76A LYS* 3.9 2.3 + - - +
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Residues in contact with GLU 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 ILE* 3.1 21.6 - - + +
72A LEU* 3.2 14.4 + - - +
73A ARG 3.9 1.9 - - - +
74A GLN* 1.3 80.3 - - + +
76A LYS* 1.3 62.3 + - - +
79A LEU* 3.7 22.3 - - + +
137A LYS* 2.6 43.2 + - - -
141A PRO 3.8 8.0 - - - +
145A PHE* 4.3 4.5 - - - -
146A LEU 4.9 1.6 + - - +
186A PRO* 3.8 16.2 - - + +
217A ARG* 2.9 25.2 + - - -
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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