Contacts of the helix formed by residues 97 - 111 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46K LEU* 4.2 18.1 - - + +
47K ASP* 3.7 22.7 + - - -
50K ASN* 3.2 11.0 - - + +
80K ILE* 5.2 11.2 - - + -
83K LEU* 3.8 32.1 - - + +
93K THR* 3.1 39.6 + - + +
94K TYR 3.6 3.1 - - - -
96K THR* 1.3 100.6 - - + +
98K ARG* 1.3 64.4 + - - +
99K HIS 3.1 3.3 + - - -
100K ILE* 3.3 28.0 + - + -
101K LEU* 2.9 29.0 + - + +
47L ASP* 4.7 7.9 + - - -
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Residues in contact with ARG 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I ARG* 3.2 51.7 - - + +
55I ASP* 4.1 9.6 - - - +
98J ARG* 4.1 8.1 - - - +
2006J SO4 2.7 41.4 + - - -
50K ASN* 3.5 2.2 + - - +
94K TYR* 3.1 18.1 + - - +
95K THR* 3.1 45.7 + - - +
96K THR 3.6 1.2 - - - -
97K TYR* 1.3 78.2 - - - +
99K HIS* 1.3 75.3 + - + +
101K LEU* 3.3 7.5 + - - +
102K ARG* 3.2 23.2 + - - +
54L ARG* 4.1 2.4 - - - +
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Residues in contact with HIS 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I ARG* 4.6 10.9 + - + -
99I HIS* 3.7 31.2 + + - -
102I ARG* 5.9 1.8 + - - -
50K ASN* 2.9 41.5 + - - +
51K LEU* 5.2 0.4 - - - -
53K LEU* 3.6 12.5 + - - +
54K ARG* 3.5 42.9 + - + +
98K ARG* 1.3 89.2 - - + +
100K ILE* 1.3 66.8 + - - +
101K LEU 3.2 1.1 - - - -
102K ARG* 3.2 11.9 + - - +
103K TRP* 3.1 22.3 + - - +
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Residues in contact with ILE 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K LEU* 3.3 44.4 - - + +
49K LEU* 4.1 15.3 - - + -
50K ASN* 3.0 29.4 - - + +
53K LEU* 4.0 8.4 - - + +
80K ILE* 3.9 16.4 - - + -
97K TYR* 3.6 24.0 - - + +
99K HIS* 1.3 75.3 - - - +
101K LEU* 1.3 52.1 + - - +
103K TRP* 3.1 11.6 + - + +
104K ILE* 2.7 56.7 + - + +
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Residues in contact with LEU 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K ILE* 3.9 13.9 - - + -
94K TYR* 3.4 56.8 - - + +
97K TYR* 2.9 18.5 + - + +
98K ARG* 3.4 9.2 - - - +
99K HIS 3.2 0.2 - - - -
100K ILE* 1.3 77.1 - - + +
102K ARG* 1.3 63.9 + - - +
104K ILE* 3.8 4.8 - - + +
105K ASP* 2.9 24.1 + - - +
119K LEU* 3.3 33.2 - - + -
121K ILE* 5.2 15.5 - - + +
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Residues in contact with ARG 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I ARG 3.8 18.8 + - - +
55I ASP* 3.7 25.4 - - - +
56I ASN 3.9 1.6 - - - -
57I THR* 3.0 42.6 + - - +
102I ARG* 3.6 34.9 - - - +
53K LEU* 3.0 37.4 + - - +
56K ASN 3.1 17.8 + - - -
57K THR* 3.3 20.8 + - - +
58K PHE* 5.8 0.4 - - - -
98K ARG 3.2 9.3 + - - +
99K HIS* 3.2 9.8 + - - +
101K LEU* 1.3 76.1 - - - +
103K TRP* 1.3 67.9 + - - +
105K ASP* 3.3 6.8 + - - +
106K TYR* 3.1 25.0 + - - +
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Residues in contact with TRP 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K LEU* 4.3 8.1 - - + -
53K LEU* 3.6 33.4 - - + -
57K THR 4.1 10.1 - - - -
58K PHE* 4.4 7.0 - + - -
59K ILE* 3.5 19.2 - - + +
69K ASP* 2.9 47.6 + - - -
72K VAL* 3.8 12.6 - - + -
73K PHE* 3.3 31.6 - + + -
76K ALA* 4.0 18.8 - - + -
99K HIS 3.1 9.8 + - - +
100K ILE* 3.1 12.9 + - + +
102K ARG* 1.3 87.1 - - - +
104K ILE* 1.3 79.3 + - + +
106K TYR* 3.2 7.5 + - + +
107K MET* 2.8 45.6 + - + +
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Residues in contact with ILE 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73K PHE* 3.9 16.6 - - + -
76K ALA 4.8 0.4 - - - -
77K LEU* 3.9 23.1 - - + +
80K ILE* 3.9 31.9 - - + -
100K ILE* 2.7 41.1 + - + +
101K LEU* 3.8 6.3 - - + +
103K TRP* 1.3 83.6 - - + +
105K ASP* 1.3 67.0 + - - +
108K GLN* 2.9 46.4 + - - +
119K LEU* 4.2 14.1 - - + -
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Residues in contact with ASP 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I ASP 4.5 10.0 - - - +
56I ASN* 5.0 5.0 - - - +
101K LEU 2.9 14.7 + - - +
102K ARG* 3.3 13.0 + - - +
104K ILE* 1.3 76.7 - - - +
106K TYR* 1.3 62.7 + - - +
108K GLN* 3.8 11.6 + - - +
109K ASN* 2.9 40.0 + - - +
121K ILE 4.2 20.4 - - - +
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Residues in contact with TYR 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I THR* 3.6 33.9 - - + +
58I PHE* 4.2 1.9 - + - -
62I THR 4.5 2.0 - - - -
63I LEU* 2.7 60.4 + - + +
64I TYR* 4.6 4.7 - - - -
15K ILE* 4.7 1.6 - - - +
58K PHE* 3.5 40.1 - + + -
65K PRO* 4.1 8.8 - - + +
102K ARG* 3.1 9.7 + - - +
103K TRP* 3.4 11.2 - - + +
104K ILE 3.1 0.2 - - - -
105K ASP* 1.3 81.1 - - - +
107K MET* 1.3 66.5 + - - +
109K ASN 3.2 2.6 + - - -
110K LEU* 2.9 50.3 + - + +
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Residues in contact with MET 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K PHE* 4.8 1.1 - - - -
65K PRO* 4.1 8.1 - - + -
69K ASP* 3.9 15.9 - - + +
70K VAL* 3.8 43.1 - - + +
73K PHE* 3.5 26.0 - - + -
103K TRP* 2.8 44.5 + - + +
106K TYR* 1.3 81.6 - - + +
108K GLN* 1.3 59.2 + - - +
110K LEU* 4.0 23.8 - - + -
111K LEU* 2.7 43.8 + - + +
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Residues in contact with GLN 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73K PHE* 3.6 14.1 - - + -
77K LEU* 3.8 5.7 - - - +
104K ILE* 2.9 35.2 + - - +
105K ASP* 3.8 17.0 + - - +
107K MET* 1.3 77.8 - - - +
109K ASN* 1.3 63.6 + - - +
112K GLU* 3.1 5.4 + - - -
113K VAL* 3.0 45.6 + - + +
118K LYS* 3.3 28.7 - - + +
119K LEU* 2.8 45.1 + - - +
121K ILE 4.6 4.9 + - - -
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Residues in contact with ASN 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I LEU* 3.9 22.1 - - + +
105K ASP* 2.9 34.6 + - - +
106K TYR 3.2 3.5 + - - +
107K MET 3.2 0.4 - - - -
108K GLN* 1.3 83.3 + - - +
110K LEU* 1.3 67.5 + - - +
112K GLU* 3.3 15.5 + - - +
118K LYS* 4.0 21.3 + - - +
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Residues in contact with LEU 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I LEU* 3.7 17.1 - - + +
64I TYR* 6.2 0.7 - - + -
9K LYS* 3.2 18.5 + - - -
10K PHE* 4.7 6.5 - - + -
13K LEU* 4.2 21.0 - - + +
15K ILE* 4.5 12.8 - - + -
65K PRO* 3.5 34.1 - - + -
106K TYR* 2.9 32.2 + - + +
107K MET* 3.8 27.1 - - + +
109K ASN* 1.3 79.3 - - - +
111K LEU* 1.3 69.4 + - + +
112K GLU* 3.9 1.9 - - - +
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Residues in contact with LEU 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K LEU* 3.8 38.1 - - + +
9K LYS* 3.4 22.8 - - + +
10K PHE* 3.9 33.9 - - + +
13K LEU* 4.9 1.3 - - + -
70K VAL* 4.0 18.8 - - + -
73K PHE* 4.0 12.8 - - + -
107K MET* 2.7 40.2 + - + +
110K LEU* 1.3 89.4 - - + +
112K GLU* 1.3 71.6 + - - +
113K VAL* 3.4 4.2 - - + -
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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