Contacts of the helix formed by residues 68 - 80 (chain A) in PDB entry 3M6L
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 ALA 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ALA* 4.0 21.1 - - + -
32A PRO* 4.2 14.6 - - + -
35A LEU* 4.3 12.3 - - + -
63A PHE* 3.9 19.1 - - + -
65A GLY* 3.0 14.6 + - - +
66A GLY 3.0 2.0 - - - -
67A HIS* 1.3 76.6 - - + +
69A SER* 1.3 63.1 + - - +
70A ALA 3.3 3.1 - - - -
71A LEU* 3.0 17.9 + - + +
72A LEU 3.4 8.0 + - - -
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Residues in contact with SER 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 5.5 0.2 - - - -
66A GLY 3.1 16.2 + - - -
67A HIS 3.1 4.1 + - - -
68A ALA* 1.3 77.9 - - - +
70A ALA* 1.3 65.1 + - - +
72A LEU* 3.1 5.4 + - - +
73A TYR* 2.9 44.2 + - - -
91A PHE* 3.4 14.6 - - - -
92A ARG* 5.1 0.2 + - - -
100A GLY 2.8 23.6 + - - -
102A PRO* 4.0 19.1 - - - -
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Residues in contact with ALA 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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17A SER* 3.6 28.7 - - - +
20A MSE 3.8 26.3 - - + +
21A VAL* 4.4 6.5 - - + -
28A HIS 5.1 1.3 - - - +
32A PRO* 4.6 5.4 - - + -
67A HIS 4.9 0.8 + - - -
68A ALA 3.2 1.2 + - - -
69A SER* 1.3 82.3 + - - +
71A LEU* 1.3 57.4 + - - +
73A TYR* 3.8 1.3 - - - +
74A SER* 2.8 33.4 + - - -
91A PHE* 4.0 15.7 - - + -
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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
----------------------------------------------------------
13A LEU* 3.8 28.7 - - + +
17A SER* 3.5 11.9 + - - +
32A PRO* 3.9 29.6 - - + +
35A LEU* 3.5 38.4 - - + +
36A ALA* 4.4 3.4 - - + -
39A LEU* 3.5 27.6 - - + -
63A PHE* 4.0 13.5 - - + -
68A ALA* 3.0 11.6 + - + +
70A ALA* 1.3 76.4 - - - +
72A LEU* 1.3 65.0 + - - +
74A SER* 3.3 3.3 + - - -
75A PHE* 3.0 23.0 + - - +
149A LEU* 5.3 0.4 - - + -
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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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61A LEU* 4.5 11.9 - - + +
63A PHE* 3.6 48.6 - - + +
68A ALA 3.4 2.8 + - - +
69A SER* 3.1 10.6 + - - +
71A LEU* 1.3 75.3 - - - +
73A TYR* 1.3 61.4 - - + +
75A PHE* 3.2 8.0 + - + +
76A LEU* 2.9 55.2 + - + +
102A PRO* 3.8 32.3 - - + -
108A GLY 5.3 2.9 - - - +
109A VAL* 4.2 16.8 - - + -
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Residues in contact with TYR 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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20A MSE 4.2 2.7 - - + -
69A SER* 2.9 29.3 + - - +
70A ALA 3.8 3.6 - - - +
72A LEU* 1.3 77.4 - - + +
74A SER* 1.3 67.1 + - - +
76A LEU* 3.3 5.1 + - + -
77A HIS* 3.0 24.9 + - - +
83A LEU* 3.7 23.3 - - + +
88A LEU* 3.7 18.7 - - + +
91A PHE* 3.8 16.6 - + - -
98A THR* 3.6 32.5 - - + -
99A PRO* 2.5 45.1 + - + +
101A HIS 3.6 6.6 + - - -
102A PRO* 3.7 9.5 - - + +
103A GLU 4.6 0.2 + - - -
106A THR* 4.5 15.9 + - + -
109A VAL* 4.7 11.7 - - + -
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Residues in contact with SER 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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13A LEU* 3.9 16.6 - - - -
16A LEU* 3.4 31.0 - - - +
17A SER* 3.6 9.1 + - - -
20A MSE 3.6 7.8 - - - -
70A ALA 2.8 23.7 + - - -
71A LEU 3.5 5.8 - - - -
73A TYR* 1.3 77.7 - - - +
75A PHE* 1.3 55.9 + - - +
77A HIS* 3.4 1.7 + - - +
78A LEU* 2.9 34.8 + - - +
88A LEU* 4.2 11.6 - - - +
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Residues in contact with PHE 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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13A LEU* 3.8 7.5 - - + +
39A LEU* 3.8 30.1 - - + -
43A SER* 3.7 29.2 - - - -
46A LEU* 4.0 28.7 - - + -
48A HIS* 4.0 13.5 - + - -
61A LEU* 4.2 18.6 - - + -
71A LEU 3.0 17.3 + - - +
72A LEU* 3.5 8.3 - - + +
74A SER* 1.3 73.4 - - - +
76A LEU* 1.3 77.8 + - + +
78A LEU* 3.3 2.4 + - - +
79A SER* 2.9 54.0 + - - -
290A PHE* 4.3 17.0 - + - -
2001A GOL 6.0 0.2 - - - -
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Residues in contact with LEU 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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61A LEU* 6.2 1.1 - - + -
72A LEU* 2.9 47.4 + - + +
73A TYR* 3.3 5.4 + - + +
75A PHE* 1.3 79.6 - - + +
77A HIS* 1.3 63.1 + - - +
79A SER 3.4 0.2 + - - -
80A GLY 3.3 4.5 + - - -
81A TYR* 3.1 69.7 + - + +
83A LEU* 4.1 18.2 - - + -
106A THR* 4.6 1.8 - - + -
107A LEU 4.0 17.0 - - - +
108A GLY 4.0 20.0 - - - +
109A VAL* 4.3 9.4 - - + -
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Residues in contact with HIS 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 TYR 3.0 17.4 + - - +
74A SER 3.7 3.6 - - - +
76A LEU* 1.3 78.6 - - - +
78A LEU* 1.3 65.9 + - + +
79A SER 3.3 0.2 + - - -
80A GLY* 3.3 9.9 + - - -
81A TYR 4.8 0.7 - - - +
83A LEU* 2.8 33.9 - - + +
84A SER* 3.5 12.0 - - - -
85A LEU* 3.4 23.9 + - + +
88A LEU* 3.9 24.6 - - + +
282A ILE* 3.5 32.3 - - + +
287A LYS* 5.2 7.6 + - - -
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Residues in contact with LEU 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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12A THR* 3.9 15.9 - - + -
13A LEU* 3.5 26.2 - - + -
16A LEU* 3.9 11.4 - - + -
74A SER 2.9 21.2 + - - +
75A PHE 4.0 2.7 - - - +
77A HIS* 1.3 78.9 - - - +
79A SER* 1.4 59.6 + - - +
80A GLY 3.6 0.3 + - - -
282A ILE* 3.6 47.3 - - + -
287A LYS* 4.6 6.9 - - + +
290A PHE* 3.4 45.7 - - + +
291A GLU* 3.4 15.1 + - - +
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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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48A HIS* 4.2 3.4 - - - -
50A PRO* 3.2 18.1 - - - +
75A PHE* 2.9 47.4 + - - -
76A LEU 4.1 2.5 - - - -
77A HIS 3.2 0.2 - - - -
78A LEU* 1.4 76.0 - - - +
80A GLY* 1.3 59.4 + - - +
81A TYR* 3.7 17.7 - - - -
290A PHE* 3.6 15.8 + - - +
291A GLU* 4.6 1.3 - - - -
293A ALA* 3.7 17.6 - - - +
294A VAL* 3.4 9.7 - - - +
2001A GOL 5.4 0.5 + - - -
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Residues in contact with GLY 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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50A PRO* 3.6 8.9 - - - +
51A LYS* 2.9 33.4 + - - +
76A LEU 3.3 3.0 + - - -
77A HIS 3.3 9.5 + - - -
78A LEU 3.3 1.4 + - - -
79A SER* 1.3 79.6 - - - +
81A TYR* 1.3 65.5 + - - +
291A GLU* 5.7 2.2 - - - -
294A VAL* 3.8 11.0 - - - -
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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