Contacts of the helix formed by residues 94 - 112 (chain E) 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 94 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E TYR* 2.6 25.1 + - - +
92E ARG 3.7 0.4 + - - -
93E VAL* 1.4 75.6 - - - +
95E PRO* 1.3 71.3 - - - +
96E VAL* 3.3 18.9 + - - +
97E ASN* 2.9 37.4 - - - +
98E PHE* 4.2 0.6 + - - -
37H TRP* 2.7 32.9 + - - +
99H ASP* 3.6 4.0 - - + +
101H GLU* 3.7 13.5 - - - +
102H ASN* 4.0 14.9 + - - -
105H LEU* 4.4 10.4 - - - +
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Residues in contact with PRO 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E VAL 3.3 5.6 - - - +
94E ASP* 1.3 91.2 - - - +
96E VAL* 1.3 62.2 + - - +
97E ASN 2.7 6.3 + - - -
98E PHE* 3.1 28.3 + - + +
99E LYS* 3.8 4.5 + - - +
137E THR* 3.1 34.8 - - + -
140E TYR* 4.2 8.3 - - + -
37H TRP* 4.6 13.5 - - + +
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Residues in contact with VAL 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ASP* 3.3 8.1 + - - +
95E PRO* 1.3 72.5 - - - +
97E ASN* 1.3 58.7 - - - +
99E LYS* 3.0 8.6 - - - +
100E LEU* 2.7 45.4 - - + +
99G LYS* 6.2 3.4 - - - +
99H ASP* 4.9 0.4 - - - +
101H GLU* 2.6 58.3 - - + +
104H ARG* 5.8 1.6 - - - +
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Residues in contact with ASN 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E MET* 5.0 2.3 - - - +
38E THR* 4.1 17.2 - - - +
39E THR* 4.6 7.5 - - - +
42E TYR* 3.2 17.1 - - - -
93E VAL* 4.4 4.0 - - + -
94E ASP* 2.9 25.0 - - - +
95E PRO 2.7 0.2 - - - -
96E VAL* 1.3 80.0 + - - +
98E PHE* 1.3 63.7 + - - +
99E LYS 3.0 4.9 - - - -
100E LEU* 3.2 13.4 + - + +
101E LEU 3.0 14.9 + - - -
142E HEM 2.9 26.5 - - + +
99H ASP* 2.1 42.7 + - - +
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Residues in contact with PHE 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E HIS* 4.2 11.7 - + - -
93E VAL* 4.4 7.9 - - + -
94E ASP 4.4 1.6 - - - -
95E PRO* 3.1 25.1 + - + +
97E ASN* 1.3 77.4 - - - +
99E LYS* 1.3 59.8 + - - +
100E LEU 3.0 0.2 + - - -
101E LEU* 3.9 1.6 - - - -
102E SER* 2.3 36.4 + - - -
133E SER* 3.4 31.4 - - - +
136E LEU* 3.7 17.9 - - + -
137E THR* 3.1 28.3 - - - +
140E TYR* 4.0 17.0 - - - -
142E HEM 2.8 64.6 - + + -
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Residues in contact with LYS 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E PRO 3.8 3.5 + - - +
96E VAL* 3.0 9.6 - - + +
98E PHE* 1.3 86.3 - - - +
100E LEU* 1.3 86.9 - - + +
102E SER* 3.9 3.5 + - - -
103E HIS* 3.5 24.7 + - - +
133E SER* 5.3 0.6 - - - -
108F ASN* 4.0 22.4 - - - +
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E MET* 4.1 7.4 - - - -
36E PHE* 4.1 37.9 - - + -
38E THR* 5.1 13.2 - - + -
39E THR* 6.6 0.2 - - - -
96E VAL* 2.7 40.8 - - + +
97E ASN* 3.2 10.2 + - + +
98E PHE 3.1 0.8 - - - -
99E LYS* 1.3 111.7 - - + +
101E LEU* 1.5 56.5 + - - +
102E SER 3.6 0.2 + - - -
103E HIS* 3.6 13.7 - - - +
104E CYS* 3.4 13.7 - - - -
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ALA* 3.8 9.2 - - + +
29E LEU* 2.9 39.9 - - + +
32E MET* 3.6 18.1 - - + -
62E VAL* 4.6 18.2 - - + -
66E LEU* 6.3 0.2 - - + -
97E ASN 3.0 17.2 + - - +
98E PHE 3.4 1.2 + - - +
100E LEU* 1.5 69.9 - - - +
102E SER* 1.3 51.4 - - - +
103E HIS 3.4 0.2 - - - -
104E CYS* 3.0 35.4 - - + +
105E LEU* 2.5 32.0 - - + +
142E HEM 4.8 25.8 - - + -
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Residues in contact with SER 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E PHE* 2.3 29.9 + - - -
99E LYS* 3.9 3.9 + - - -
101E LEU* 1.3 71.9 - - - +
103E HIS* 1.2 59.0 - - - +
105E LEU* 3.2 22.5 - - - +
106E LEU* 3.5 10.4 - - - +
129E LEU* 2.7 46.8 + - - +
130E ALA* 5.5 0.9 - - - -
133E SER* 3.5 7.8 + - - -
142E HEM 6.0 2.1 - - - +
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Residues in contact with HIS 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E PHE* 4.0 15.7 - + + -
99E LYS* 3.5 17.1 + - - +
100E LEU* 3.6 12.8 - - - +
102E SER* 1.2 74.6 - - - +
104E CYS* 1.4 63.8 + - - +
105E LEU 3.3 0.4 - - - -
106E LEU* 3.4 16.9 - - + +
107E VAL* 3.2 33.6 - - + +
108F ASN* 3.6 38.9 + - + +
109F VAL* 6.2 1.1 - - + -
111F VAL* 4.5 2.5 - - + -
112F CYS* 4.7 4.7 - - - -
127F GLN* 4.3 4.8 + - - -
131F GLN* 2.7 34.7 + - - -
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Residues in contact with CYS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ALA* 3.9 9.0 - - - -
31E ARG* 4.4 3.8 - - + -
32E MET* 3.5 28.9 - - - +
36E PHE* 4.7 7.2 - - - -
100E LEU 3.4 13.7 - - - -
101E LEU* 3.0 35.4 - - + +
103E HIS* 1.4 66.8 - - - +
105E LEU* 1.4 54.5 + - - +
107E VAL* 3.0 12.9 - - - +
108E THR* 1.8 47.4 + - - +
127F GLN* 4.5 4.5 - - - +
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E TRP* 5.2 4.7 - - + -
28E ALA* 4.3 10.5 - - + -
62E VAL* 6.2 1.6 - - + -
66E LEU* 4.0 25.6 - - + -
101E LEU* 2.5 52.0 - - + +
102E SER* 3.2 18.2 - - - +
104E CYS* 1.4 77.0 - - - +
106E LEU* 1.1 55.3 + - - +
108E THR* 3.0 8.5 - - - -
109E LEU* 2.3 56.7 + - + +
128E PHE* 6.1 0.7 - - + -
129E LEU* 3.6 20.9 - - + -
142E HEM 6.0 3.6 - - + -
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E SER 3.5 14.8 - - - +
103E HIS* 3.4 19.1 - - + +
105E LEU* 1.1 70.9 - - - +
107E VAL* 1.3 44.9 + - - -
108E THR 2.8 2.7 - - - -
109E LEU* 2.7 13.1 + - - +
110E ALA* 2.4 25.7 + - - +
117E PHE* 4.6 10.8 - - + -
122E HIS* 3.6 28.3 - - + +
125E LEU* 3.9 38.4 - - + +
126E ASP* 3.7 28.3 - - + +
129E LEU* 4.5 9.2 - - + -
112F CYS* 4.3 13.0 - - - -
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Residues in contact with VAL 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ARG* 4.0 8.7 + - - +
103E HIS* 3.2 32.1 - - + +
104E CYS 3.0 14.6 - - - +
106E LEU* 1.3 57.9 - - - +
108E THR* 1.4 56.0 - - - +
110E ALA* 2.6 25.1 - - - +
111E ALA* 2.8 27.4 - - - +
111F VAL* 3.9 18.6 - - + -
112F CYS* 3.3 23.7 - - - -
115F ALA* 3.7 6.9 - - + +
122F PHE* 5.1 3.6 - - + -
127F GLN* 3.3 35.2 - - - +
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Residues in contact with THR 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E TYR* 4.2 23.6 - - + +
27E GLU* 3.7 29.8 - - + +
28E ALA* 3.9 8.9 - - - +
31E ARG* 4.1 8.3 - - - +
104E CYS* 1.8 45.9 + - - +
105E LEU* 3.0 11.6 + - - +
107E VAL* 1.4 87.7 - - - +
109E LEU* 1.3 66.6 - - - +
110E ALA 3.2 0.3 + - - -
111E ALA* 3.3 7.4 + - - +
112E HIS* 3.5 23.3 - - + -
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Residues in contact with LEU 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ALA* 5.2 1.1 - - + +
14E TRP* 3.8 38.1 - - + -
17E VAL* 4.1 19.7 - - + -
24E TYR* 3.9 32.1 - - + -
105E LEU* 2.3 48.6 + - + +
106E LEU 2.7 8.6 + - - +
108E THR* 1.3 68.0 - - - +
110E ALA* 1.1 48.6 + - - -
111E ALA 3.5 0.2 - - - -
112E HIS* 3.7 2.1 + - - -
113E LEU* 2.2 39.9 - - + +
117E PHE* 5.2 3.5 - - - +
125E LEU* 3.7 33.9 - - + -
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Residues in contact with ALA 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU 2.4 24.0 + - - +
107E VAL* 2.6 35.7 - - - +
109E LEU 1.1 62.1 - - - -
111E ALA* 1.3 54.9 + - + -
112E HIS 3.3 5.0 + - - -
113E LEU 3.9 10.9 + - - +
114E PRO* 4.4 0.7 - - - +
117E PHE* 4.1 29.8 - - + -
112F CYS* 4.7 9.0 - - - +
115F ALA 4.1 4.8 - - - +
116F HIS* 3.4 23.3 + - - +
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Residues in contact with ALA 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ARG* 4.5 13.7 - - - +
107E VAL 2.8 19.7 - - - +
108E THR 3.3 5.1 + - - +
110E ALA* 1.3 70.5 - - - +
112E HIS* 1.3 66.7 + - + +
113E LEU 3.8 0.7 - - - -
114E PRO* 5.1 5.3 - - - +
115F ALA* 3.6 26.0 - - + +
116F HIS 5.3 0.2 - - - -
119F GLY* 3.5 32.4 - - - +
120F LYS* 4.2 1.4 + - - +
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Residues in contact with HIS 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLU* 4.6 11.7 - - + -
24E TYR* 3.7 35.3 + + + +
27E GLU* 2.5 46.5 + - - -
108E THR* 3.5 26.0 - - + +
109E LEU* 3.7 0.4 + - - -
110E ALA 3.3 0.6 - - - -
111E ALA* 1.3 86.2 + - + +
113E LEU* 1.2 85.6 + - + +
114E PRO* 3.0 12.8 - - - +
120F LYS* 6.0 5.6 - - + -
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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