Contacts of the helix formed by residues 67 - 82 (chain M) in PDB entry 6FF7
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 67 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M VAL* 3.6 33.6 - - - +
39M LEU* 6.1 2.9 - - - -
64M LEU 4.4 2.4 + - - -
66M CYS* 1.3 73.8 - - - +
68M TYR* 1.3 51.5 + - - +
69M LYS* 3.0 6.3 - - - -
70M LEU* 2.7 37.8 + - - +
71M TRP* 3.1 7.8 + - - -
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Residues in contact with TYR 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M LEU 5.3 0.6 + - - -
65M PRO* 4.8 5.6 - - + -
66M CYS 3.0 11.3 - - - +
67M SER* 1.3 75.4 - - - +
69M LYS* 1.3 56.4 + - - +
71M TRP* 3.2 14.0 + - - +
72M TYR* 2.9 25.1 + - - +
101M ARG* 4.0 35.0 - - + +
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Residues in contact with LYS 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M CYS 3.9 8.6 + - - +
67M SER 2.9 1.2 + - - +
68M TYR* 1.3 77.4 - - - +
70M LEU* 1.3 57.8 + - - +
72M TYR* 2.9 11.1 + - - +
73M ARG* 2.9 24.1 + - - +
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Residues in contact with LEU 70 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M LEU* 5.2 15.4 - - + +
67M SER* 2.7 22.5 + - - +
69M LYS* 1.3 76.0 - - - +
71M TRP* 1.3 55.9 + - - +
73M ARG* 3.3 10.2 + - + +
74M TYR* 2.9 28.2 + - - +
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Residues in contact with TRP 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M LEU* 6.0 1.5 - - - +
60M ALA* 5.6 8.3 - - + -
67M SER 3.1 6.5 + - - +
68M TYR* 3.3 21.3 - - + +
69M LYS 3.1 0.2 - - - -
70M LEU* 1.3 76.8 - - - +
72M TYR* 1.3 57.6 + - - +
74M TYR* 3.7 6.7 - - - +
75M LEU* 2.9 26.2 + - - +
97M ASN* 6.0 1.1 - - + +
101M ARG* 5.1 9.2 - - + -
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Residues in contact with TYR 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M TYR 2.9 11.7 + - - +
69M LYS* 2.9 12.3 + - - +
71M TRP* 1.3 75.9 - - - +
73M ARG* 1.3 59.8 + - - +
75M LEU* 3.5 8.4 - - - +
76M LYS* 2.9 27.9 + - - +
98M CYS* 5.9 7.4 - - + +
112M LEU* 6.3 3.1 - - + -
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Residues in contact with ARG 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69M LYS 2.9 11.5 + - - +
70M LEU* 3.3 11.9 + - - +
72M TYR* 1.3 77.9 - - - +
74M TYR* 1.3 57.5 + - - +
76M LYS* 3.2 7.8 + - - +
77M ALA* 2.9 28.1 + - - +
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Residues in contact with TYR 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M LEU* 5.8 8.1 - - + +
42M ILE* 6.4 2.2 - - + -
43M GLU* 6.0 5.6 - - + -
70M LEU 2.9 17.3 + - - +
71M TRP* 3.9 7.6 - - - +
73M ARG* 1.3 74.9 - - - +
75M LEU* 1.3 57.9 + - - +
77M ALA* 4.1 6.6 - - - +
78M ARG* 2.9 31.0 + - - +
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Residues in contact with LEU 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71M TRP 2.9 19.7 + - - +
72M TYR* 3.5 10.3 - - - +
73M ARG 3.2 0.6 - - - -
74M TYR* 1.3 77.5 - - - +
76M LYS* 1.3 57.3 + - - +
78M ARG* 4.5 3.8 - - - -
79M ARG* 2.9 30.5 + - - +
94M ASP* 4.1 27.8 - - + +
97M ASN* 5.5 6.3 - - + -
98M CYS* 5.6 4.9 - - + +
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Residues in contact with LYS 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72M TYR 2.9 15.8 + - - +
73M ARG* 3.2 7.6 + - - +
75M LEU* 1.3 76.1 - - - +
77M ALA* 1.3 59.4 + - - +
79M ARG* 3.8 5.0 - - - +
80M ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M ARG 2.9 16.3 + - - +
74M TYR* 4.1 6.7 - - - +
76M LYS* 1.3 75.4 - - - +
78M ARG* 1.3 59.2 + - - +
80M ALA* 3.3 5.7 + - - +
81M GLN* 2.9 29.5 + - - +
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Residues in contact with ARG 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74M TYR 2.9 21.0 + - - +
75M LEU* 4.3 4.7 - - - +
77M ALA* 1.3 75.9 - - - +
79M ARG* 1.3 58.5 + - - +
81M GLN* 3.9 5.4 - - - +
82M VAL* 2.9 33.1 + - - +
94M ASP* 6.5 0.2 - - + -
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Residues in contact with ARG 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75M LEU 2.9 22.3 + - - +
76M LYS* 4.0 5.4 - - - +
78M ARG* 1.3 76.5 - - - +
80M ALA* 1.3 58.4 + - - +
82M VAL* 3.8 3.7 - - - +
83M LYS* 3.1 26.9 + - - +
90M PRO* 5.1 11.2 - - + +
91M ALA* 6.3 0.4 - - - -
94M ASP* 4.3 16.1 - - + +
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Residues in contact with ALA 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76M LYS 2.9 18.8 + - - +
77M ALA* 3.7 7.0 - - - +
79M ARG* 1.3 76.2 - - - +
81M GLN* 1.3 62.9 + - - +
83M LYS* 3.5 17.2 + - - +
84M HIS 4.8 0.9 + - - -
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Residues in contact with GLN 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77M ALA 2.9 17.9 + - - +
78M ARG* 4.0 5.2 - - - +
80M ALA* 1.3 77.5 - - - +
82M VAL* 1.3 59.2 + - - +
83M LYS 3.3 0.7 + - - -
84M HIS* 4.2 10.0 + - - +
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Residues in contact with VAL 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M ARG 2.9 19.0 + - - +
79M ARG 3.8 0.9 - - - -
81M GLN* 1.3 73.2 - - - +
83M LYS* 1.3 64.0 + - - +
84M HIS 3.1 2.7 - - - -
85M ARG* 3.1 30.5 + - + +
90M PRO* 3.8 25.1 - - + +
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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