Contacts of the helix formed by residues 75 - 92 (chain M) in PDB entry 3TDD
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 75 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E LYS* 3.6 13.8 + - - +
10M SER* 2.9 50.6 + - - -
40M ASN* 3.6 12.0 - - - +
41M THR* 4.2 2.0 - - - -
71M ALA 4.3 3.7 - - + -
74M LEU* 1.3 76.2 - - - +
76M PRO* 1.3 73.7 - - + +
77M SER* 3.8 10.1 - - - +
78M TYR* 3.1 52.2 + - + -
79M ILE* 3.2 13.9 + - - +
105M GLN* 3.7 16.7 + - - +
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Residues in contact with PRO 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M ASN* 3.3 28.5 - - - +
41M THR* 3.0 29.6 - - + +
75M GLU* 1.3 84.6 - - + +
77M SER* 1.3 62.2 + - - +
79M ILE* 3.2 4.0 + - + +
80M PHE* 2.9 23.6 + - - +
101M VAL* 4.0 3.1 - - - +
103M GLY* 3.9 4.7 - - - -
104M VAL 3.7 19.1 - - - +
105M GLN* 2.8 20.0 - - - +
109M PHE* 4.0 24.2 - - + -
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Residues in contact with SER 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E PHE 4.0 1.1 - - - +
104E ASN* 4.4 17.0 + - - +
75M GLU* 3.8 2.3 - - - +
76M PRO* 1.3 81.7 - - - +
78M TYR* 1.3 77.5 + - - +
80M PHE* 3.8 1.2 - - - +
81M GLU* 3.0 26.9 + - - +
105M GLN* 2.9 28.6 + - - -
109M PHE* 3.7 23.7 - - - -
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Residues in contact with TYR 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E PHE* 3.1 34.5 - - + +
104E ASN 3.5 11.2 - - - -
105E ARG* 3.5 56.3 + - + +
106E LYS 5.5 0.2 + - - -
143E LYS* 3.2 34.5 + - + +
62M LEU* 5.5 0.2 - - - -
71M ALA* 3.7 10.7 - + + +
74M LEU* 4.0 11.7 - - + -
75M GLU* 3.1 41.6 + - + +
77M SER* 1.3 84.7 + - - +
79M ILE* 1.3 64.2 + - - +
81M GLU* 3.9 1.7 - - - +
82M TYR* 3.0 25.1 + - - +
105M GLN* 5.8 0.2 - - - -
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Residues in contact with ILE 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M VAL* 3.2 37.9 - - + +
41M THR* 3.6 26.0 - - + +
43M VAL* 4.1 19.1 - - + -
59M LEU* 3.8 25.4 - - + -
62M LEU* 4.4 12.8 - - + +
74M LEU* 4.2 18.2 - - + +
75M GLU 3.2 9.6 + - - +
76M PRO 3.6 6.3 - - - +
78M TYR* 1.3 77.1 - - - +
80M PHE* 1.3 63.1 + - - +
82M TYR* 3.4 6.8 - - - +
83M LEU* 3.1 25.8 + - + +
101M VAL* 4.9 1.6 - - + -
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Residues in contact with PHE 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76M PRO 2.9 10.5 + - - +
77M SER 3.8 2.0 - - - +
79M ILE* 1.3 72.5 - - - +
81M GLU* 1.3 73.8 + - - +
82M TYR 2.8 2.3 + - - -
83M LEU* 2.9 4.4 + - - +
84M ALA* 2.7 48.6 + - + +
101M VAL* 3.8 28.0 - - + +
109M PHE* 3.5 24.9 - + + -
111M ARG* 3.3 63.3 - - + -
112M TYR 3.5 19.1 - - - -
113M VAL* 4.1 11.7 - - + -
119M THR* 3.6 14.6 - - + -
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Residues in contact with GLU 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E SER 5.3 0.2 - - - +
101E LEU 3.5 10.9 - - - +
102E VAL 3.0 16.9 - - - +
103E PHE 3.8 9.6 - - - -
104E ASN* 3.6 27.0 - - + +
57L LYS* 2.8 27.5 + - - +
77M SER 3.0 16.1 + - - +
78M TYR 3.9 0.2 - - - +
80M PHE* 1.3 93.8 - - - +
82M TYR* 1.3 55.6 + - - +
84M ALA* 3.7 5.6 - - - +
85M THR* 2.8 32.6 + - - -
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Residues in contact with TYR 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E TYR* 6.2 0.2 - - - -
102E VAL* 3.3 16.3 + - + -
103E PHE* 3.6 35.4 - + + -
58M LEU* 4.1 37.9 + - + +
59M LEU* 5.1 1.1 - - + -
62M LEU* 3.6 27.8 - - + -
78M TYR 3.0 17.0 + - - +
79M ILE* 3.4 6.1 - - - +
80M PHE 2.8 1.2 + - - -
81M GLU* 1.3 74.3 - - - +
83M LEU* 1.3 84.7 + - + +
85M THR* 3.0 7.6 + - + -
86M VAL* 3.0 40.3 + - + +
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Residues in contact with LEU 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M VAL* 4.0 27.1 - - + -
55M ILE* 3.7 27.1 - - + +
58M LEU* 5.3 6.3 - - + -
59M LEU* 4.3 12.3 - - + -
79M ILE* 3.1 20.9 + - + +
80M PHE* 2.9 7.4 + - - +
82M TYR* 1.3 94.7 - - + +
84M ALA* 1.3 58.9 + - - +
86M VAL* 3.2 7.3 + - + +
87M MET* 2.8 37.1 + - + +
99M ILE* 4.3 16.4 - - + -
101M VAL* 4.3 13.2 - - + -
113M VAL* 4.8 8.7 - - + -
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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
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80M PHE* 2.7 43.2 + - + +
81M GLU* 3.7 9.9 - - - +
83M LEU* 1.3 72.2 - - - +
85M THR* 1.3 64.5 + - - +
87M MET* 3.2 1.6 + - - +
88M TYR* 3.1 25.1 + - - +
113M VAL* 3.8 23.0 - - + +
117M GLY* 4.9 1.2 - - - +
119M THR* 4.2 7.0 - - + -
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Residues in contact with THR 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E LEU 4.1 4.0 + - - -
102E VAL* 3.6 35.1 + - + -
57L LYS* 4.7 5.2 + - - -
81M GLU 2.8 19.3 + - - -
82M TYR* 3.0 11.9 + - + -
84M ALA* 1.3 76.9 - - - +
86M VAL* 1.3 66.1 + - + +
88M TYR* 3.3 4.1 + - - +
89M GLN* 3.0 47.4 + - + +
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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
----------------------------------------------------------
54M HIS* 5.9 0.7 - - - +
58M LEU* 4.6 13.9 - - + -
82M TYR* 3.0 47.0 + - + +
83M LEU* 3.5 10.5 - - + +
85M THR* 1.3 79.5 - - + +
87M MET* 1.3 64.6 + - + +
89M GLN* 3.2 12.9 + - - +
90M ARG* 2.9 31.9 + - + +
95M LEU* 3.7 26.0 - - + -
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Residues in contact with MET 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M ILE* 4.7 1.8 - - - -
83M LEU* 2.8 27.7 + - + +
84M ALA 3.7 4.0 - - - +
86M VAL* 1.3 74.2 - - - +
88M TYR* 1.3 58.5 + - - +
90M ARG* 3.5 5.1 + - - +
91M ARG* 3.1 26.2 + - - +
95M LEU* 3.3 52.4 + - + +
97M ASN* 3.9 9.2 - - + +
99M ILE* 4.1 21.8 - - + -
113M VAL* 3.8 22.4 - - + -
114M ASN* 3.3 39.5 - - - +
115M LEU* 3.7 7.7 - - - +
117M GLY* 4.3 2.2 - - - -
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Residues in contact with TYR 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L ALA* 3.7 23.3 - - + -
51L ASP* 2.6 28.7 + - - -
54L ALA* 3.6 32.4 - - + +
90L LYS* 5.1 2.1 - - - -
95L TYR* 4.0 8.8 - + - -
84M ALA 3.1 16.7 + - - +
85M THR* 3.9 3.8 - - - +
87M MET* 1.3 74.9 - - - +
89M GLN* 1.3 69.2 + - + +
91M ARG* 3.6 19.5 + - + +
92M SER* 2.9 42.6 + - - -
116M LEU 3.7 15.0 - - - -
117M GLY* 4.0 12.7 - - - +
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Residues in contact with GLN 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M THR* 3.0 39.1 + - + +
86M VAL* 3.2 14.6 + - - +
88M TYR* 1.3 78.8 - - + +
90M ARG* 1.3 65.3 + - + +
92M SER* 3.1 53.2 + - - +
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Residues in contact with ARG 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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-7M GLN* 4.4 3.4 + - - -
51M ASP* 5.3 0.6 + - - -
54M HIS* 4.3 14.3 + - - -
86M VAL* 2.9 33.1 + - + +
87M MET* 3.8 4.9 - - - +
89M GLN* 1.3 77.3 - - + +
91M ARG* 1.3 62.6 + - - +
92M LYS* 3.2 15.4 + - - +
93M ASN* 2.7 78.6 + - - +
94M PRO* 3.9 11.3 + - + -
95M LEU* 3.6 37.0 - - + +
88N TYR* 4.9 5.7 + - - -
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Residues in contact with ARG 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-8L PHE* 3.9 20.2 - - + -
-6L PRO* 2.4 51.9 + - - +
-5L TYR* 3.9 10.5 - - - -
48L PHE* 3.3 14.1 - - - -
51L ASP* 3.2 25.0 + - - -
90L LYS* 4.6 7.7 - - - +
93L PHE* 3.7 24.0 - - - -
94L PRO 5.1 0.4 + - - -
87M MET 3.1 9.5 + - - +
88M TYR* 3.6 16.5 + - + +
90M ARG* 1.3 76.7 - - - +
92M SER* 1.3 99.9 + - - +
94M PRO* 4.4 3.5 - - - +
115M LEU 3.1 24.0 - - - +
116M LEU* 3.4 24.0 - - - +
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Residues in contact with SER 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L LYS* 5.3 3.3 + - - -
93L PHE* 3.5 23.6 - - - -
88M TYR* 2.9 40.2 + - - -
89M GLN* 3.4 9.6 - - - -
90M ARG 3.1 0.4 - - - -
91M ARG* 1.3 97.2 + - - +
92M LYS* 1.3 59.8 + - - +
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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