Contacts of the helix formed by residues 81 - 95 (chain M) in PDB entry 2DFS
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 HIS 81 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14M TRP* 4.9 0.2 - + - -
61M PRO* 3.5 27.5 - - + +
62M LEU* 3.0 39.4 + - - +
79M TYR* 3.6 25.3 + - + +
80M LEU* 1.3 78.0 - - - +
82M GLU* 1.4 66.5 + - - +
83M PRO* 4.0 11.3 - - + +
84M ALA* 2.9 21.0 + - + +
85M VAL* 3.2 14.5 + - - +
688M LEU* 5.3 0.2 - - - -
691M ILE* 5.1 3.1 - - - -
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Residues in contact with GLU 82 (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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21M VAL* 4.6 3.1 - - - +
22M TRP* 2.9 30.3 + - + +
81M HIS* 1.4 73.0 - - - +
83M PRO* 1.3 69.2 - - + +
85M VAL* 3.3 3.3 + - - +
86M LEU* 3.0 23.3 + - + +
679M VAL* 3.5 27.4 - - + +
683M ARG* 4.1 16.2 + - - +
688M LEU* 3.5 40.8 - - + +
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Residues in contact with PRO 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M TRP* 3.6 35.0 - - + -
22M TRP* 3.7 35.7 - - + +
61M PRO* 3.7 27.4 - - + -
81M HIS* 3.8 9.0 - - + +
82M GLU* 1.3 93.9 - - + +
84M ALA* 1.3 57.1 + - - +
86M LEU* 3.9 8.6 - - + +
87M HIS* 3.0 30.8 + - - +
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Residues in contact with ALA 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M TRP* 4.6 6.9 - - - +
64M ASN* 3.5 15.9 - - - +
77M LEU* 4.0 10.3 - - + +
79M TYR 3.2 27.4 - - - +
81M HIS* 2.9 19.1 + - + +
83M PRO* 1.3 77.4 - - - +
85M VAL* 1.3 59.5 + - + +
87M HIS* 4.0 5.1 - - - +
88M ASN* 3.0 31.5 + - - +
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Residues in contact with VAL 85 (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 LEU* 3.8 32.7 - - + +
77M LEU* 4.8 0.9 - - + -
80M LEU* 4.3 16.2 - - + -
81M HIS 3.2 15.5 + - - +
82M GLU 3.7 5.8 - - - +
84M ALA* 1.3 74.8 - - - +
86M LEU* 1.3 62.8 + - - +
88M ASN* 3.5 0.9 + - - +
89M LEU* 3.1 38.2 + - + +
682M LEU* 4.3 5.8 - - + -
687M VAL* 5.0 2.9 - - + -
688M LEU* 4.0 18.8 - - + -
691M ILE* 3.6 28.0 - - + -
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Residues in contact with LEU 86 (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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20M GLU 4.6 2.5 - - - +
21M VAL* 4.6 7.9 - - + -
22M TRP* 4.2 25.4 - - + -
82M GLU* 3.0 20.2 + - + +
83M PRO* 3.9 4.7 - - + +
85M VAL* 1.3 75.7 - - - +
87M HIS* 1.3 56.6 + - - +
89M LEU* 3.6 3.6 + - - +
90M LYS* 3.1 29.8 + - + +
673M PHE* 4.1 14.5 - - + -
675M GLU* 4.2 26.0 - - + +
678M ALA* 3.8 29.6 - - + -
679M VAL* 4.0 19.3 - - + +
682M LEU* 4.5 12.7 - - + +
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Residues in contact with HIS 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M TRP* 3.4 32.3 - + + -
63M ARG* 2.9 33.6 + - + -
69M VAL* 4.0 27.1 - - + +
83M PRO 3.0 20.1 + - - +
84M ALA* 4.0 5.2 - - - +
86M LEU* 1.3 72.8 - - - +
88M ASN* 1.3 64.5 + - - +
90M LYS* 3.4 11.5 + - - +
91M VAL* 3.1 42.4 + - + +
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Residues in contact with ASN 88 (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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68M LEU 4.2 1.2 + - - -
69M VAL* 4.3 8.0 - - + +
70M GLY 3.5 23.5 - - - +
71M GLU* 4.1 14.0 + - - +
73M ASP 4.9 1.2 + - - -
74M LEU* 3.4 25.0 - - + +
77M LEU* 3.9 26.3 - - + +
84M ALA 3.0 20.8 + - - +
85M VAL 3.9 3.1 - - - +
87M HIS* 1.3 75.4 - - + +
89M LEU* 1.3 63.4 + - - +
91M VAL* 3.3 23.1 - - - +
92M ARG* 3.3 25.6 + - - +
101M THR* 4.6 0.2 - - - +
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Residues in contact with LEU 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74M LEU* 4.1 16.8 - - + -
85M VAL* 3.1 36.9 + - + +
86M LEU 4.0 3.1 - - - +
88M ASN* 1.3 75.8 - - - +
90M LYS* 1.3 62.4 + - - +
92M ARG* 3.5 4.7 + - - +
93M PHE* 3.0 25.6 + - - +
101M THR* 3.6 38.1 - - + +
108M VAL* 4.6 14.6 - - + -
110M ILE* 4.2 21.0 - - + +
673M PHE* 4.3 10.5 - - + -
682M LEU* 4.3 25.1 - - + -
687M VAL* 6.1 0.2 - - + -
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Residues in contact with LYS 90 (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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20M GLU* 2.7 40.0 + - - +
86M LEU* 3.1 19.7 + - + +
87M HIS* 3.4 12.1 + - - +
89M LEU* 1.3 75.4 - - - +
91M VAL* 1.4 60.9 + - + +
93M PHE* 3.4 0.7 + - - +
94M ILE* 2.9 48.8 + - + +
95M ASP* 5.7 0.4 - - - +
673M PHE* 3.9 20.8 - - + -
675M GLU* 2.6 33.8 + - + +
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Residues in contact with VAL 91 (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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69M VAL* 4.3 17.0 - - + -
70M GLY* 4.6 11.2 - - - -
87M HIS* 3.1 34.3 + - + +
88M ASN* 3.3 20.2 - - - +
90M LYS* 1.4 77.2 - - + +
92M ARG* 1.3 62.5 + - - +
95M ASP* 3.1 44.3 + - + +
96M SER* 3.5 3.8 + - - -
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Residues in contact with ARG 92 (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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70M GLY* 2.7 46.7 + - - +
71M GLU 3.2 16.1 + - - -
72M ASN* 2.8 31.1 + - - +
88M ASN* 3.3 28.0 + - - +
89M LEU* 3.8 4.9 - - - +
91M VAL* 1.3 77.5 - - + +
93M PHE* 1.3 59.7 + - - +
96M SER* 3.5 9.0 + - - -
97M LYS 3.2 7.4 + - - -
98M LEU* 2.9 58.8 + - + +
100M TYR 2.8 24.0 + - - -
101M THR* 2.9 24.0 + - - +
110M ILE* 6.4 0.2 - - + -
136M ASP* 5.4 0.2 + - - -
137M PRO* 3.7 8.9 - - - +
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Residues in contact with PHE 93 (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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89M LEU 3.0 19.1 + - - +
90M LYS 3.7 2.9 - - - +
92M ARG* 1.3 77.1 - - - +
94M ILE* 1.3 70.8 + - + +
97M LYS* 3.4 10.4 + - - -
98M LEU 3.6 6.5 + - - +
99M ILE* 3.8 14.6 - - + -
110M ILE* 3.4 35.9 - - + -
111M ASN 3.6 20.4 - - - -
112M PRO* 4.1 1.6 - - + -
664M PRO* 3.9 11.4 - - + -
671M PHE* 3.2 74.1 - + - -
672M THR 3.9 12.1 - - - -
673M PHE* 3.7 20.4 - + + -
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Residues in contact with ILE 94 (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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90M LYS* 2.9 32.0 + - + +
93M PHE* 1.3 86.4 - - + +
95M ASP* 1.3 77.7 + - - +
97M LYS* 4.0 9.4 + - - +
671M PHE* 3.2 29.5 - - - +
672M THR* 4.3 0.9 - - + -
673M PHE* 3.9 26.9 - - + +
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Residues in contact with ASP 95 (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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90M LYS* 4.6 0.7 - - - +
91M VAL* 3.1 40.3 + - + +
94M ILE* 1.3 87.5 - - - +
96M SER* 1.3 60.5 + - - +
97M LYS* 5.3 1.6 - - - +
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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