Contacts of the helix formed by residues 97 - 111 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I LEU* 4.1 19.9 - - + +
47I ASP* 3.8 22.7 + - - -
50I ASN* 3.2 12.1 - - + +
80I ILE* 3.9 20.6 - - + -
83I LEU* 3.8 28.6 - - + +
93I THR* 3.2 37.1 + - + +
94I TYR 3.2 6.2 + - - -
96I THR* 1.3 101.2 - - + +
98I ARG* 1.3 62.5 + - - -
99I HIS 3.1 3.3 + - - -
100I ILE* 3.3 20.5 + - + -
101I LEU* 2.9 28.2 + - + +
47J ASP* 4.7 7.8 + - - -
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Residues in contact with ARG 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I ASN* 3.5 2.4 + - - +
91I LYS* 5.2 0.2 - - - +
94I TYR* 3.1 17.5 + - - +
95I THR* 3.2 40.1 + - - +
96I THR 3.7 1.2 - - - -
97I TYR* 1.3 76.4 - - - +
99I HIS* 1.3 76.9 + - + +
101I LEU* 3.4 7.8 + - - +
102I ARG* 3.1 24.1 + - - +
2005I SO4 2.8 42.6 + - - -
54J ARG* 4.4 1.6 - - - +
54K ARG* 3.4 50.8 - - + +
55K ASP* 3.7 12.0 - - - +
98L ARG* 4.8 5.1 - - - +
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Residues in contact with HIS 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I ASN* 2.9 45.6 - - - +
51I LEU* 5.2 0.4 - - - -
53I LEU* 3.7 11.2 - - + +
54I ARG* 3.5 41.6 - - + +
98I ARG* 1.3 91.3 - - + +
100I ILE* 1.3 65.1 + - - +
101I LEU 3.1 1.5 + - - -
102I ARG* 3.3 12.4 + - - +
103I TRP* 3.3 21.5 + - - +
54K ARG* 4.6 10.3 + - + -
99K HIS* 3.7 30.5 + + - -
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Residues in contact with ILE 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I LEU* 3.6 34.1 - - + +
49I LEU* 4.0 21.5 - - + -
50I ASN* 3.1 26.9 - - + +
53I LEU* 3.9 8.7 - - - +
76I ALA* 5.1 1.6 - - + -
80I ILE* 4.0 12.6 - - + -
97I TYR* 3.7 24.5 - - + +
99I HIS* 1.3 74.5 - - - +
101I LEU* 1.3 58.6 + - - +
103I TRP* 3.3 12.3 + - + +
104I ILE* 2.8 51.1 + - + +
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Residues in contact with LEU 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I ILE* 3.8 17.7 - - + -
84I VAL* 5.5 0.9 - - + -
93I THR* 4.9 0.4 - - + +
94I TYR* 3.6 61.9 - - + +
97I TYR* 2.9 23.8 + - + +
98I ARG* 3.6 7.4 - - - +
99I HIS 3.1 0.2 - - - -
100I ILE* 1.3 75.6 - - - +
102I ARG* 1.3 66.9 + - - +
104I ILE* 3.8 3.8 - - + +
105I ASP* 2.9 25.1 + - - +
119I LEU* 3.1 37.6 - - + +
121I ILE 5.0 7.4 - - - +
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Residues in contact with ARG 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I LEU* 2.6 40.4 + - - +
54I ARG* 4.4 3.0 + - - +
56I ASN 3.0 17.0 + - - -
57I THR* 3.1 19.2 + - - +
98I ARG 3.1 12.9 + - - +
99I HIS* 3.5 22.5 + - - +
101I LEU* 1.3 76.9 - - - +
103I TRP* 1.3 62.4 + - - +
105I ASP* 3.4 5.5 + - - +
106I TYR* 3.0 25.1 + - - +
53K LEU 4.1 5.1 + - - -
54K ARG 3.8 15.7 + - - +
55K ASP* 3.6 29.7 - - - +
56K ASN 4.0 3.6 - - - -
57K THR* 3.8 31.0 + - - +
99K HIS* 5.9 2.0 + - - -
102K ARG* 3.6 23.1 - - - +
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Residues in contact with TRP 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I LEU* 4.3 14.4 - - + -
53I LEU* 3.7 33.9 - - + -
57I THR 3.9 11.0 - - - +
58I PHE* 4.3 8.1 - + - -
59I ILE* 3.4 19.1 - - + +
69I ASP* 2.8 45.4 + - - -
72I VAL* 3.8 11.4 - - + -
73I PHE* 3.4 35.7 - + + -
76I ALA* 4.4 4.3 - - + -
99I HIS 3.3 12.7 + - - +
100I ILE* 3.8 11.7 - - + -
101I LEU 3.2 0.4 - - - -
102I ARG* 1.3 87.0 - - - +
104I ILE* 1.3 76.4 + - + +
106I TYR* 3.1 6.7 + - + +
107I MET* 2.8 51.2 + - + +
57K THR* 5.1 0.7 - - - -
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Residues in contact with ILE 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I PHE* 4.2 14.1 - - + -
76I ALA 4.3 1.6 - - - +
77I LEU* 3.8 26.9 - - + +
80I ILE* 3.9 24.9 - - + -
100I ILE* 2.8 44.0 + - + +
101I LEU* 3.8 5.2 - - + +
103I TRP* 1.3 82.8 - - + +
105I ASP* 1.3 57.5 + - - +
108I GLN* 2.7 59.5 + - - +
119I LEU* 3.9 20.4 - - + -
121I ILE 6.1 0.4 - - - +
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Residues in contact with ASP 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I LEU 2.9 17.0 + - - +
102I ARG* 3.4 7.4 - - - +
104I ILE* 1.3 77.1 - - - +
106I TYR* 1.3 63.1 + - - +
108I GLN* 4.1 12.5 + - - +
109I ASN* 3.0 43.7 + - - +
121I ILE* 4.2 19.1 + - - +
55K ASP 4.7 8.4 - - - +
56K ASN* 4.9 6.4 - - - +
61K SER* 5.2 5.4 + - - -
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Residues in contact with TYR 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I PHE* 3.5 39.1 - + + -
64I TYR* 5.8 1.7 - - - -
65I PRO* 4.1 17.7 - - + +
102I ARG 3.0 14.8 + - - +
103I TRP* 3.1 10.1 + - + +
105I ASP* 1.3 79.8 - - - +
107I MET* 1.3 68.7 + - - +
109I ASN* 3.2 2.3 + - - +
110I LEU* 2.8 45.2 + - + +
57K THR* 3.7 27.4 - - + +
58K PHE* 4.2 7.4 - + - -
62K THR 4.0 6.7 - - - -
63K LEU* 2.6 56.6 + - + +
64K TYR* 4.6 4.3 - - - -
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Residues in contact with MET 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I PHE* 4.8 1.3 - - - -
65I PRO* 4.1 15.7 - - + -
69I ASP* 3.9 22.7 - - + +
70I VAL* 3.9 19.1 - - + +
73I PHE* 3.4 23.8 - - + -
103I TRP* 2.8 49.8 + - + +
106I TYR* 1.3 89.1 - - + +
108I GLN* 1.3 58.4 + - - +
110I LEU* 4.1 10.5 - - + -
111I LEU* 2.9 57.0 + - + +
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Residues in contact with GLN 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I PHE* 3.6 19.3 - - + -
77I LEU* 3.6 4.7 - - - +
104I ILE* 2.7 39.1 + - - +
105I ASP* 3.8 17.8 + - - +
107I MET* 1.3 74.1 - - - +
109I ASN* 1.3 68.4 + - - +
112I GLU* 3.3 2.4 + - - -
113I VAL* 2.9 39.2 + - + +
118I LYS* 3.5 27.6 - - + +
119I LEU 2.9 43.2 + - - +
121I ILE 4.5 4.2 + - - +
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Residues in contact with ASN 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I ASP* 3.0 32.4 + - - +
106I TYR* 3.2 3.4 + - - +
107I MET 3.2 0.4 - - - -
108I GLN* 1.3 82.8 + - - +
110I LEU* 1.3 67.9 + - - +
112I GLU* 3.2 15.6 + - - +
118I LYS* 4.0 15.9 + - - +
61K SER 5.9 1.0 + - - -
63K LEU* 4.2 17.0 - - + +
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Residues in contact with LEU 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I PRO* 3.9 26.7 - - + -
70I VAL* 5.6 1.8 - - + -
106I TYR* 2.8 41.7 + - + +
107I MET* 3.7 16.2 - - + +
109I ASN* 1.3 73.5 - - - +
111I LEU* 1.3 80.9 + - + +
112I GLU* 3.3 7.2 + - - +
63K LEU* 3.7 19.9 - - + +
64K TYR* 4.5 17.7 - - + +
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Residues in contact with LEU 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I VAL* 4.4 24.0 - - + -
73I PHE* 3.9 27.1 - - + -
107I MET* 2.9 34.4 + - + +
110I LEU* 1.3 92.9 - - + +
112I GLU* 1.3 73.4 + - - +
113I VAL* 3.2 11.3 + - + +
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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
------------------------------------------------------------
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