Contacts of the helix formed by residues 99 - 117 (chain H) in PDB entry 1HBS
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 ASP 99 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E THR* 2.8 24.2 + - - +
41E THR* 4.1 6.0 + - + -
42E TYR* 2.9 29.6 + - + +
94E ASP* 3.6 4.4 - - + +
96E VAL* 5.3 0.3 - - - +
97E ASN* 2.1 42.8 + - - +
41H PHE* 4.0 6.9 - - - -
97H HIS 3.6 2.8 + - - -
98H VAL* 1.3 70.3 - - - +
100H PRO* 1.4 59.9 - - + +
101H GLU* 2.5 36.9 + - + +
102H ASN* 2.3 40.4 + - - +
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Residues in contact with PRO 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E THR* 3.3 28.0 - - - +
41E THR* 4.2 4.5 - - + -
98H VAL 2.9 7.5 - - - +
99H ASP* 1.4 83.0 - - + +
101H GLU* 1.4 64.9 + - - +
102H ASN 3.0 1.4 + - - -
103H PHE* 3.1 29.8 + - + +
104H ARG* 3.6 14.0 + - - +
138H ALA 5.1 2.6 - - - +
142H ALA* 3.3 33.8 - - + +
145H TYR* 4.0 21.8 - - + -
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Residues in contact with GLU 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ASP* 3.7 16.4 - - - +
96E VAL* 2.6 50.5 - - + +
99H ASP* 2.5 27.0 + - + +
100H PRO* 1.4 64.8 - - - +
102H ASN* 1.2 50.7 + - - +
104H ARG* 2.8 57.1 + - - +
105H LEU* 3.5 14.0 + - + +
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Residues in contact with ASN 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TYR* 5.5 1.8 + - - -
94E ASP* 4.0 17.4 + - - -
31H LEU* 5.3 0.8 - - - +
37H TRP* 5.4 1.8 - - - +
38H THR* 5.1 8.1 - - - +
41H PHE* 3.5 23.4 - - - -
98H VAL* 2.5 21.8 - - + +
99H ASP* 2.3 30.0 + - - +
101H GLU* 1.2 66.1 - - - +
103H PHE* 1.2 60.9 - - - +
104H ARG 2.9 0.9 - - - -
105H LEU* 2.7 12.8 + - - +
106H LEU* 2.4 36.7 + - - +
147H HEM 3.4 27.7 - - + +
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Residues in contact with PHE 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H HIS* 2.7 59.0 - + + -
98H VAL* 3.8 8.7 - - + -
100H PRO* 3.1 31.9 + - + +
102H ASN* 1.2 79.1 - - - +
104H ARG* 1.3 61.8 + - - +
106H LEU* 4.4 1.5 - - - +
107H GLY* 3.0 21.3 + - - -
134H VAL* 4.8 1.2 - - - +
138H ALA* 4.2 24.8 - - - +
141H LEU* 3.7 42.0 - - + -
145H TYR* 3.6 10.5 - + - -
147H HEM 3.3 48.5 - + + +
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Residues in contact with ARG 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E VAL* 5.8 2.2 - - - +
100H PRO* 3.6 9.6 + - - +
101H GLU* 2.8 45.7 + - - +
103H PHE* 1.3 77.7 - - - +
105H LEU* 1.5 45.9 + - + +
107H GLY* 4.0 0.9 - - - -
108H ASN* 3.5 23.1 + - - +
135H ALA* 6.0 4.3 - - + -
138H ALA* 4.5 16.3 + - + +
139H ASN* 4.3 26.0 + - - +
142H ALA* 6.2 3.0 - - - +
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ASP* 4.4 22.9 - - - +
31H LEU* 4.2 6.6 - - + +
35H TYR* 3.3 59.4 - - + +
37H TRP* 5.2 4.7 - - + +
38H THR* 5.9 2.0 - - + -
101H GLU* 3.5 18.5 + - - +
102H ASN* 2.7 16.3 + - - +
104H ARG* 1.5 56.1 - - - +
106H LEU* 1.3 66.4 - - - +
107H GLY 2.8 5.6 - - - -
108H ASN* 3.1 10.1 + - + +
109H VAL* 3.1 21.3 + - - +
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Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ALA* 4.7 8.8 - - + +
28H LEU* 3.9 31.6 - - + +
31H LEU* 2.7 39.9 - - + +
67H VAL* 5.2 4.0 - - + -
68H LEU* 5.7 4.7 - - + -
102H ASN 2.4 28.8 + - - +
103H PHE 4.8 0.2 - - - +
105H LEU* 1.3 69.8 - - - +
107H GLY* 1.3 64.3 - - - +
109H VAL* 2.9 22.1 + - - +
110H LEU* 3.2 22.0 + - + -
147H HEM 3.4 46.0 - - + -
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Residues in contact with GLY 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H PHE 3.0 13.1 + - - -
104H ARG 4.0 1.8 - - - -
105H LEU 2.8 0.8 - - - -
106H LEU* 1.3 83.9 - - - +
108H ASN* 1.3 63.3 + - - +
109H VAL 3.0 4.9 - - - -
110H LEU* 3.3 10.3 + - - +
111H VAL* 3.2 25.1 - - - +
134H VAL* 3.3 30.8 - - - +
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Residues in contact with ASN 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G PHE* 5.8 1.8 - - - -
99G LYS* 6.3 1.6 - - - +
100G LEU* 6.1 2.4 - - - +
103G HIS* 3.0 49.4 + - + +
35H TYR* 5.4 4.7 - - - +
104H ARG 3.5 13.9 + - - +
105H LEU* 3.1 16.3 + - + +
107H GLY* 1.3 80.0 - - - +
109H VAL* 1.3 72.8 - - - +
110H LEU 3.0 1.7 + - - -
111H VAL* 3.8 0.8 + - - -
112H CYS* 3.8 8.5 + - - -
131H GLN* 2.7 35.0 + - - +
134H VAL* 5.6 0.7 - - - +
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Residues in contact with VAL 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G HIS* 6.0 0.4 - - - +
122G HIS* 4.3 24.4 - - + +
27H ALA* 4.0 13.5 - - - +
30H ARG* 3.9 21.1 - - + +
31H LEU* 4.4 11.7 - - + -
34H VAL* 4.4 2.9 - - + -
35H TYR* 3.4 37.5 - - + +
105H LEU 3.1 5.5 + - - +
106H LEU* 2.9 12.2 + - - +
108H ASN* 1.3 87.7 - - - +
110H LEU* 1.4 51.4 - - - +
112H CYS* 3.7 2.2 + - - +
113H VAL* 2.7 37.4 + - + +
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H TRP* 4.7 9.6 - - + -
23H VAL* 5.3 7.9 - - + +
27H ALA* 5.8 3.1 - - + -
68H LEU* 4.6 22.7 - - + -
71H PHE* 3.9 40.2 - - + -
106H LEU* 3.2 21.9 + - + +
107H GLY* 3.3 13.4 + - - +
108H ASN 3.0 1.4 - - - -
109H VAL* 1.4 73.7 - - - +
111H VAL* 1.4 74.2 + - + +
112H CYS 3.1 2.5 - - - -
113H VAL* 4.1 9.4 - - + -
114H LEU* 2.7 53.5 + - + +
130H TYR* 4.5 4.7 - - + -
134H VAL* 5.0 3.8 - - + -
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Residues in contact with VAL 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G HIS* 4.5 2.5 - - + -
107G VAL* 3.7 7.6 - - + +
107H GLY 3.2 19.3 - - - +
108H ASN 4.3 5.6 - - - +
109H VAL 3.4 0.2 - - - -
110H LEU* 1.4 84.6 - - + +
112H CYS* 1.4 56.8 - - - +
114H LEU* 5.1 0.7 - - - -
115H ALA* 3.2 6.4 + - - -
122H PHE* 2.8 47.6 - - + -
127H GLN* 4.1 26.7 - - + +
130H TYR* 4.1 11.2 - - + +
131H GLN* 4.3 23.3 - - + +
134H VAL* 3.9 20.9 - - + -
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Residues in contact with CYS 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G HIS* 3.8 18.2 - - - -
106G LEU* 4.6 9.9 - - - -
107G VAL* 2.2 48.0 - - + -
110G ALA* 3.6 11.4 - - + +
117G PHE* 5.1 7.9 - - + -
122G HIS* 5.3 7.9 - - + -
108H ASN 3.8 3.7 + - - -
109H VAL 3.7 5.2 + - - +
110H LEU 3.1 0.2 - - - -
111H VAL* 1.4 74.4 - - - +
113H VAL* 1.3 59.8 + - - +
114H LEU 2.9 0.9 - - - -
115H ALA* 2.7 33.7 + - + +
116H HIS* 3.1 8.9 + - - +
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Residues in contact with VAL 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G PHE* 6.1 0.4 - - - -
122G HIS* 5.7 1.7 - - + -
23H VAL* 4.8 17.9 - - + +
26H GLU* 3.4 50.2 - - + +
27H ALA* 4.4 7.9 - - + +
30H ARG* 3.7 14.8 - - - +
109H VAL* 2.7 35.6 + - + +
110H LEU* 3.5 9.8 + - + +
112H CYS* 1.3 72.2 - - - +
114H LEU* 1.4 53.9 - - - +
116H HIS* 3.6 8.6 + - - +
117H HIS* 2.7 31.6 + - - +
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Residues in contact with LEU 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H LEU* 3.7 23.8 - - + -
15H TRP* 4.9 3.6 - - + -
18H VAL* 4.5 7.0 - - + -
110H LEU* 2.7 39.9 + - + +
111H VAL 3.9 0.4 - - - -
113H VAL* 1.4 74.7 - - - +
115H ALA* 1.4 65.5 + - - +
117H HIS* 3.0 20.6 - - + +
118H PHE* 2.9 51.9 - - + +
122H PHE* 3.9 18.7 - - + -
130H TYR* 3.6 43.7 - - + +
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Residues in contact with ALA 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G VAL* 3.1 22.7 - - + +
110G ALA* 3.1 22.2 - - + -
111G ALA* 3.5 3.3 - - + +
111H VAL 3.2 7.0 + - - -
112H CYS* 2.7 36.3 + - + +
114H LEU* 1.4 75.3 - - - +
116H HIS* 1.2 48.7 + - - +
117H HIS 2.9 0.2 - - - -
119H GLY* 2.9 34.6 + - - +
122H PHE* 4.0 12.3 - - + +
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Residues in contact with HIS 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G ALA* 3.2 22.9 - - + +
111G ALA* 4.5 1.1 - - - +
114G PRO* 2.4 54.7 + - + +
115G ALA* 4.3 5.5 - - - +
117G PHE* 3.5 23.4 + + + +
26H GLU* 3.4 25.6 + - - -
30H ARG* 3.8 11.9 + - - -
112H CYS 3.4 12.3 - - - +
113H VAL* 3.7 6.1 + - - +
115H ALA* 1.2 67.8 - - - +
117H HIS* 1.3 67.3 + - - +
118H PHE 3.6 0.2 - - - -
119H GLY* 3.8 6.2 + - - +
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Residues in contact with HIS 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LYS 3.7 15.7 + - - -
18H VAL* 4.7 2.6 - - + +
19H ASN* 5.3 8.3 - - + -
22H GLU* 6.1 1.3 - - - -
23H VAL* 4.8 19.0 - - + +
113H VAL 2.7 18.1 + - - +
114H LEU* 3.0 18.6 - - - +
115H ALA 2.9 1.4 - - - -
116H HIS* 1.3 85.2 - - - +
118H PHE* 1.4 113.9 + + + +
119H GLY 3.4 0.7 - - - -
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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