Contacts of the helix formed by residues 97 - 111 (chain M) in PDB entry 2HQT
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 TYR 97 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46M LEU* 4.1 18.1 - - + +
47M ASP* 3.9 21.9 + - - -
50M ASN* 3.2 11.0 - - + -
80M ILE* 4.3 15.7 - - + -
83M LEU* 3.8 30.6 - - + +
93M THR* 3.1 40.6 + - + +
94M TYR 3.6 4.0 - - - -
96M THR* 1.3 99.3 - - + +
98M ARG* 1.3 64.2 + - - +
99M HIS 3.1 3.0 + - - -
100M ILE* 3.3 27.6 + - + -
101M LEU* 3.0 27.9 + - + +
47N ASP* 4.6 7.4 + - - -
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Residues in contact with ARG 98 (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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50M ASN* 3.4 3.2 + - - +
94M TYR* 3.2 16.0 + - - +
95M THR* 3.4 41.5 + - - +
96M THR 3.7 1.4 - - - -
97M TYR* 1.3 76.5 - - - +
99M HIS* 1.3 78.0 + - + +
101M LEU* 3.3 6.7 + - - +
102M ARG* 3.0 24.8 + - - +
2008M SO4 2.8 36.2 + - - -
54N ARG* 3.8 5.9 - - - +
54O ARG* 3.4 49.0 - - + +
55O ASP* 4.0 12.2 - - - +
98P ARG* 4.0 3.4 - - - +
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Residues in contact with HIS 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M ASN* 2.8 52.2 + - - +
51M LEU* 5.3 0.2 - - - -
53M LEU* 3.6 11.2 - - + +
54M ARG* 3.5 48.3 - - + +
98M ARG* 1.3 85.4 - - + +
100M ILE* 1.3 67.2 + - - +
101M LEU 3.1 1.1 - - - -
102M ARG* 3.4 14.9 + - - +
103M TRP* 3.2 21.8 + - - +
54O ARG* 4.7 8.9 + - + -
99O HIS* 3.9 22.4 + + - -
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Residues in contact with ILE 100 (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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46M LEU* 3.7 42.2 - - + +
49M LEU* 4.0 15.0 - - + -
50M ASN* 3.1 21.3 + - + +
53M LEU* 3.9 8.9 - - + +
76M ALA* 5.1 1.8 - - + -
80M ILE* 4.1 11.7 - - + -
97M TYR* 3.3 30.9 + - + +
99M HIS* 1.3 76.6 - - - +
101M LEU* 1.3 52.2 + - + +
103M TRP* 3.3 11.8 + - + +
104M ILE* 2.7 59.3 + - + +
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Residues in contact with LEU 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M ILE* 4.1 26.0 - - + -
94M TYR* 3.4 59.5 - - + +
97M TYR* 3.0 20.3 + - + +
98M ARG* 3.5 6.7 - - - +
99M HIS 3.1 0.2 - - - -
100M ILE* 1.3 74.1 - - + +
102M ARG* 1.3 67.1 + - - +
104M ILE* 3.9 11.5 - - + +
105M ASP* 2.9 26.3 + - - +
119M LEU* 4.9 10.1 - - + -
120M GLU 5.8 0.7 - - - +
121M ILE* 5.8 6.1 - - + -
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Residues in contact with ARG 102 (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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53M LEU* 2.6 32.5 + - - +
54M ARG* 4.5 2.8 + - - +
56M ASN 3.0 25.3 + - - -
57M THR* 3.1 20.0 + - - +
98M ARG 3.0 13.4 + - - +
99M HIS* 3.5 21.7 + - - +
101M LEU* 1.3 76.1 - - - +
103M TRP* 1.3 62.4 + - - +
105M ASP* 3.4 5.9 - - - +
106M TYR* 3.1 25.5 + - - +
53O LEU 4.1 0.6 + - - -
54O ARG 3.8 17.5 + - - +
55O ASP* 3.8 21.6 - - - +
56O ASN 3.9 3.8 - - - -
57O THR* 3.8 36.7 + - - +
99O HIS* 6.0 1.2 + - - -
102O ARG* 3.7 27.6 - - - +
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Residues in contact with TRP 103 (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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49M LEU* 4.4 8.7 - - + -
53M LEU* 3.6 32.1 - - + -
57M THR 3.9 11.7 - - - -
58M PHE* 4.2 8.1 - + - -
59M ILE* 3.4 29.7 - - + +
69M ASP* 3.0 38.9 + - - -
72M VAL* 4.0 6.1 - - + -
73M PHE* 3.5 29.8 - + + -
76M ALA* 4.1 13.9 - - + -
99M HIS 3.2 13.5 + - - +
100M ILE* 3.7 9.2 - - + -
102M ARG* 1.3 82.1 - - - +
104M ILE* 1.3 80.5 + - + +
106M TYR* 3.2 6.5 + - - +
107M MET* 2.8 54.5 + - + +
57O THR* 5.2 0.7 - - - -
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Residues in contact with ILE 104 (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 PHE* 3.8 16.7 - - + -
76M ALA* 4.5 1.1 - - + -
77M LEU* 4.0 27.1 - - + +
80M ILE* 3.7 29.4 - - + -
100M ILE* 2.7 45.3 + - + +
101M LEU* 3.9 10.8 - - + +
103M TRP* 1.3 83.7 - - + +
105M ASP* 1.3 61.5 + - - +
108M GLN* 2.8 48.3 + - - +
119M LEU* 4.1 10.8 - - + -
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Residues in contact with ASP 105 (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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101M LEU 2.9 18.6 + - - +
102M ARG* 3.4 7.3 - - - +
104M ILE* 1.3 79.5 - - - +
106M TYR* 1.3 62.0 - - - +
108M GLN* 3.6 15.1 + - - +
109M ASN* 2.8 40.8 + - - -
121M ILE 5.5 8.9 - - - -
55O ASP 4.6 10.0 - - - +
56O ASN* 5.0 5.4 - - - +
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Residues in contact with TYR 106 (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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58M PHE* 3.6 34.9 - + + -
64M TYR* 5.7 1.9 - - - -
65M PRO* 4.4 6.5 - - + +
102M ARG 3.1 11.4 + - - +
103M TRP* 3.4 10.1 - - - +
105M ASP* 1.3 81.8 - - - +
107M MET* 1.3 66.8 + - + +
109M ASN* 3.4 0.6 + - - -
110M LEU* 2.9 54.3 + - + +
57O THR* 3.7 30.1 - - + +
58O PHE* 4.2 10.4 - + - -
62O THR 4.1 6.3 - - - -
63O LEU* 2.6 57.6 + - + +
64O TYR* 4.3 5.5 - - - -
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Residues in contact with MET 107 (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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58M PHE* 4.8 1.8 - - - -
65M PRO* 4.1 22.2 - - + -
69M ASP* 3.7 31.4 - - + +
70M VAL* 4.2 7.0 - - + +
73M PHE* 3.5 23.3 - - + -
103M TRP* 2.8 52.1 + - + +
106M TYR* 1.3 86.5 - - + +
108M GLN* 1.3 58.1 + - - +
110M LEU* 4.2 8.1 - - + -
111M LEU* 2.9 58.6 + - + +
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Residues in contact with GLN 108 (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 PHE* 3.6 18.6 - - + -
77M LEU* 3.9 2.4 - - - +
104M ILE* 2.8 29.5 + - - +
105M ASP* 3.6 22.4 + - - +
107M MET* 1.3 74.4 - - - +
109M ASN* 1.3 66.4 + - - +
112M GLU 3.2 2.8 + - - -
113M VAL* 2.8 42.1 + - + +
118M LYS* 3.3 26.1 - - + +
119M LEU* 2.7 52.3 + - - +
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Residues in contact with ASN 109 (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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105M ASP* 2.8 40.2 + - - +
106M TYR* 3.6 3.4 - - - +
107M MET 3.3 0.4 - - - -
108M GLN* 1.3 87.5 - - - +
110M LEU* 1.3 66.6 + - - +
112M GLU* 3.2 19.6 + - - +
118M LYS* 4.0 18.9 + - - +
63O LEU* 4.0 18.8 - - + +
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Residues in contact with LEU 110 (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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65M PRO* 3.7 30.5 - - + -
106M TYR* 2.9 38.3 + - + +
107M MET* 3.7 11.9 - - + +
109M ASN* 1.3 78.2 - - - +
111M LEU* 1.3 77.0 + - + +
112M GLU* 3.2 15.2 + - - +
63O LEU* 3.7 19.5 - - + +
64O TYR* 3.8 23.8 - - + +
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Residues in contact with LEU 111 (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 VAL* 4.3 24.5 - - + -
73M PHE* 4.2 16.4 - - + -
107M MET* 2.9 39.0 + - + +
108M GLN 3.9 0.2 - - - -
110M LEU* 1.3 93.0 - - + +
112M GLU* 1.3 69.5 + - - +
113M VAL* 3.0 13.0 + - + +
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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