Contacts of the helix formed by residues 78 - 99 (chain M) in PDB entry 3P4P
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 78 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76M LEU 3.8 5.4 + - - +
77M CYS* 1.3 70.4 - - - +
79M GLN* 1.3 61.4 + - - +
80M ASP* 3.2 17.9 - - - +
81M VAL* 3.0 32.6 + - + +
82M VAL* 3.3 11.8 - - - +
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Residues in contact with GLN 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M PHE* 3.5 36.1 - - + -
70M VAL* 4.1 16.9 - - + +
75M TRP* 3.6 28.2 + - - +
77M CYS 3.2 10.6 + - - +
78M GLU* 1.3 71.0 - - - +
80M ASP* 1.3 56.8 + - - +
82M VAL* 3.4 8.4 + - - -
83M ASP* 3.1 24.6 + - - +
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Residues in contact with ASP 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M GLU* 3.5 14.9 - - - +
79M GLN* 1.3 75.0 - - - +
81M VAL* 1.3 91.5 + - - +
83M ASP* 3.4 14.6 + - - +
84M TYR* 3.6 11.4 + - - +
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Residues in contact with VAL 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M GLU* 3.0 24.8 + - + +
80M ASP* 1.3 98.1 + - - +
82M VAL* 1.3 61.1 + - + +
84M TYR* 3.5 8.7 + - + +
85M PHE* 3.2 27.7 + - + +
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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
----------------------------------------------------------
66M PHE* 3.3 28.9 - - + +
69M THR* 3.8 35.4 - - + +
70M VAL* 4.6 2.7 - - + -
77M CYS* 3.9 23.1 - - + -
78M GLU 3.3 15.0 + - - +
79M GLN* 3.7 10.3 - - - +
80M ASP 3.2 0.6 - - - -
81M VAL* 1.3 78.4 - - + +
83M ASP* 1.3 63.7 + - - +
85M PHE* 4.2 10.5 - - + -
86M VAL* 3.0 24.0 + - + +
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Residues in contact with ASP 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M PHE* 4.5 15.6 - - + +
79M GLN 3.1 15.8 + - - +
80M ASP* 3.4 8.0 + - - +
81M VAL 3.3 0.4 - - - -
82M VAL* 1.3 77.5 - - - +
84M TYR* 1.3 59.0 + - - +
86M VAL* 3.7 2.6 - - - +
87M HIS* 2.5 55.6 + - - -
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Residues in contact with TYR 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M ASP 3.6 8.1 + - - +
81M VAL* 3.5 11.4 + - + +
83M ASP* 1.3 77.1 - - - +
85M PHE* 1.3 69.3 + - + +
87M HIS* 3.0 13.1 + - - -
88M HIS* 2.9 71.8 + + + +
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Residues in contact with PHE 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M ALA 5.4 1.6 - - - -
65M HIS* 4.6 15.9 - + - -
69M THR* 5.1 12.6 - - + -
81M VAL* 3.2 18.0 + - + +
82M VAL* 3.8 13.0 - - + +
84M TYR* 1.3 85.8 - - + +
86M VAL* 1.3 66.2 + - + +
88M HIS* 3.4 3.5 + - - +
89M CYS* 3.1 54.1 + - - -
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Residues in contact with VAL 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M VAL* 4.7 2.6 - - - +
62M PHE* 3.1 62.4 - - + +
65M HIS* 3.4 35.1 + - + +
66M PHE* 3.5 13.9 - - + +
69M THR* 5.1 1.3 - - - +
82M VAL* 3.0 16.0 + - + +
83M ASP* 3.7 3.8 - - - +
85M PHE* 1.3 82.1 - - + +
87M HIS* 1.3 78.0 + - + +
89M CYS* 3.8 5.6 + - - +
90M PRO* 3.6 11.8 - - - +
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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
----------------------------------------------------------
62M PHE* 3.6 45.0 - + + +
83M ASP* 2.5 51.7 + - - +
84M TYR* 3.0 5.6 + - - +
86M VAL* 1.3 92.5 - - + +
88M HIS* 1.3 69.6 + - + +
89M CYS 3.4 0.4 - - - -
90M PRO* 3.8 10.4 - - - +
91M THR* 4.9 4.0 + - - -
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Residues in contact with HIS 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M TYR* 2.9 67.8 + + + +
85M PHE* 3.4 3.8 + - - +
87M HIS* 1.3 87.2 - - + +
89M CYS* 1.3 66.6 + - - +
90M PRO 3.5 0.7 - - - -
91M THR* 3.6 13.5 + - - +
92M GLU* 3.4 30.8 + - + +
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Residues in contact with CYS 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M ALA 3.7 12.3 - - - +
54M ALA* 3.6 24.9 - - + +
55M VAL 4.9 0.4 - - - +
65M HIS* 4.9 4.9 - - + -
85M PHE* 3.1 60.1 + - - +
86M VAL* 3.9 5.6 - - - +
88M HIS* 1.3 77.4 - - - +
90M PRO* 1.4 72.5 - - + +
91M THR 3.3 0.3 + - - -
92M GLU* 3.3 5.2 + - - +
93M MET* 3.1 24.9 + - - +
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Residues in contact with PRO 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M ALA* 4.0 8.3 - - + -
55M VAL* 3.8 29.2 - - + +
62M PHE* 3.8 22.2 - - + -
86M VAL 3.6 12.1 - - - +
87M HIS 3.8 7.4 - - - +
88M HIS 3.8 2.0 - - - -
89M CYS* 1.4 93.7 - - + +
91M THR* 1.3 57.9 + - - +
93M MET* 4.4 1.8 - - + +
94M THR* 2.8 29.5 + - - -
125M TRP* 5.1 3.7 - - + -
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Residues in contact with THR 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M HIS 4.9 2.9 + - - -
88M HIS* 3.6 17.6 + - - +
89M CYS 3.3 0.8 - - - -
90M PRO* 1.3 79.0 - - - +
92M GLU* 1.3 72.3 + - - +
94M THR* 2.8 11.1 + - - +
95M GLN* 2.7 35.5 + - + +
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Residues in contact with GLU 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M ARG* 2.4 36.0 + - - +
88M HIS* 3.4 20.2 + - + +
89M CYS* 3.3 5.0 + - - +
91M THR* 1.3 100.3 - - - +
93M MET* 1.3 73.8 + - + +
95M GLN* 3.1 11.8 + - - +
96M LEU* 2.9 27.6 + - + +
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Residues in contact with MET 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M SER* 3.8 23.8 - - - +
53M ALA 4.6 3.1 - - - +
54M ALA* 3.9 11.4 - - + -
89M CYS* 3.1 19.7 + - - +
90M PRO 4.4 1.1 - - - +
92M GLU* 1.3 90.6 - - + +
94M THR* 1.3 60.2 + - - +
96M LEU* 3.4 27.7 + - + +
97M GLU* 3.4 16.8 + - - +
103M TRP* 3.4 20.9 + - + -
125M TRP* 3.5 53.7 - - + -
135M MET* 4.8 2.5 - - - -
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Residues in contact with THR 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M PRO 2.8 17.5 + - - -
91M THR* 2.8 14.8 + - - +
93M MET* 1.3 79.6 - - - +
95M GLN* 1.3 56.8 + - - +
97M GLU* 3.6 7.5 + - + +
98M LEU* 3.0 42.7 + - + +
125M TRP* 4.4 11.3 - - - -
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Residues in contact with GLN 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M ARG* 4.9 1.3 - - - +
91M THR* 2.7 17.1 + - + +
92M GLU* 3.1 23.5 + - - +
94M THR* 1.3 73.5 - - - +
96M LEU* 1.3 60.7 + - - +
98M LEU* 3.2 26.2 + - - +
99M TRP* 3.0 72.2 + - + +
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Residues in contact with LEU 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M GLU 2.9 15.9 + - - +
93M MET* 3.4 28.9 - - + +
94M THR 3.4 0.2 - - - -
95M GLN* 1.3 72.4 - - + +
97M GLU* 1.3 67.3 + - - +
99M TRP* 2.9 24.4 + - + +
100M GLY 3.1 0.5 + - - -
101M CYS* 3.1 22.4 + - + +
103M TRP* 3.6 11.4 - - + -
135M MET* 3.6 35.2 - - + +
138M THR* 3.8 11.5 - - + +
139M LEU* 3.5 38.8 - - + -
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Residues in contact with GLU 97 (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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93M MET 3.4 10.2 + - - +
94M THR* 3.6 11.2 - - - +
95M GLN 3.3 0.2 - - - -
96M LEU* 1.3 79.3 - - - +
98M LEU* 1.3 78.6 + - - +
100M GLY* 2.9 20.4 + - - -
101M CYS 3.8 14.4 + - - +
103M TRP* 3.8 15.3 - - + +
105M ARG* 2.9 34.4 + - - +
111M VAL* 5.2 3.1 - - + -
125M TRP* 5.5 1.8 - - + -
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Residues in contact with LEU 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94M THR* 3.0 32.1 - - + +
95M GLN* 3.2 31.6 + - - +
96M LEU 3.2 0.8 - - - -
97M GLU* 1.3 103.1 + - - +
99M TRP* 1.3 62.0 + - + +
100M GLY* 3.1 7.7 + - - -
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Residues in contact with TRP 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M ARG* 3.9 21.1 - - - -
21M ILE* 3.6 35.2 - - + -
25M GLN* 4.6 17.9 - - - +
95M GLN* 3.0 46.5 + - + +
96M LEU* 2.9 21.9 + - + +
98M LEU* 1.3 79.4 - - - +
100M GLY* 1.3 56.7 + - - +
101M CYS 3.6 0.2 - - - -
138M THR* 3.5 15.0 - - + +
139M LEU* 3.5 34.1 - - + -
142M THR* 3.5 39.8 + - + +
145M GLN* 5.4 3.0 - - - +
146M PHE* 5.5 1.4 - + - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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