Contacts of the helix formed by residues 100 - 119 (chain D) in PDB entry 1SHR
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 PRO 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D VAL 3.4 5.1 - - - +
99D ASP* 1.3 94.4 - - - +
101D GLU* 1.3 64.6 + - - +
103D PHE* 2.9 36.1 + - + +
104D ARG* 3.7 3.5 + - - +
142D ALA* 3.8 21.2 - - + +
144D LYS* 3.5 31.0 - - - +
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Residues in contact with GLU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A VAL* 5.8 2.5 - - + -
99C LYS* 5.4 3.9 + - - -
37D TRP* 6.4 0.2 - - + -
99D ASP* 3.1 17.2 + - + +
100D PRO* 1.3 77.6 - - - +
102D ASN* 1.3 64.9 + - - +
104D ARG* 2.5 60.3 + - - +
105D LEU* 3.3 22.3 + - + +
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Residues in contact with ASN 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASP* 2.8 24.6 + - - +
31D LEU* 4.6 0.9 - - - +
37D TRP* 3.0 25.9 + - - -
38D THR* 3.9 10.7 - - + +
41D PHE* 4.7 3.6 - - - -
98D VAL* 4.0 6.1 - - + +
99D ASP* 3.0 32.0 + - - +
101D GLU* 1.3 78.0 - - - +
103D PHE* 1.3 63.8 + - - +
105D LEU* 3.2 18.8 + - - +
106D LEU* 3.1 18.2 + - - +
747D HEM 3.3 29.7 - - + +
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Residues in contact with PHE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D HIS* 3.7 44.6 - + + -
93D CYS* 5.3 2.0 - - + -
98D VAL* 3.9 24.7 - - + -
100D PRO* 2.9 33.1 + - + +
102D ASN* 1.3 77.5 - - - +
104D ARG* 1.3 62.2 + - - +
106D LEU 3.4 0.9 + - - -
107D GLY* 3.1 17.8 + - - -
138D ALA* 3.9 20.2 - - + +
141D LEU* 3.7 28.0 - - + -
142D ALA* 3.7 21.8 - - + -
747D HEM 3.7 44.6 - - + +
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Residues in contact with ARG 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LYS* 4.3 31.3 - - - +
100C LEU* 6.2 2.6 - - - +
100D PRO 3.7 2.7 + - - +
101D GLU* 2.5 47.2 + - - +
103D PHE* 1.3 76.7 - - - +
105D LEU* 1.3 74.9 + - - +
107D GLY* 3.2 2.5 + - - +
108D ASN* 2.9 59.7 + - - +
138D ALA* 4.0 13.6 - - + +
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 4.2 3.6 - - + -
35D TYR* 3.8 41.7 - - + +
37D TRP* 3.8 22.0 - - + -
101D GLU* 3.4 20.6 - - + +
102D ASN* 3.2 28.2 + - - +
104D ARG* 1.3 109.2 - - - +
106D LEU* 1.3 61.7 + - - +
108D ASN* 3.3 6.1 + - - +
109D VAL* 3.0 29.2 + - - +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ALA* 4.0 31.4 - - + +
28D LEU* 4.8 3.4 - - + -
31D LEU* 4.0 27.3 - - + +
67D VAL* 4.0 17.5 - - + -
71D PHE* 5.0 4.5 - - + -
102D ASN 3.1 12.5 + - - +
103D PHE 3.8 7.2 - - - +
104D ARG 3.3 0.2 - - - -
105D LEU* 1.3 73.2 - - - +
107D GLY* 1.3 66.8 + - - +
109D VAL* 3.2 3.7 + - + -
110D LEU* 2.9 22.3 + - + +
747D HEM 3.4 50.0 - - + -
748D CYN 4.7 5.6 - - - +
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Residues in contact with GLY 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D PHE* 4.7 8.0 - - - -
103D PHE 3.1 14.1 + - - -
104D ARG* 3.2 4.4 + - - -
106D LEU* 1.3 77.4 - - - +
108D ASN* 1.3 57.5 + - - +
110D LEU* 3.3 7.2 + - - +
111D VAL* 3.0 30.5 + - - +
134D VAL* 3.9 29.2 - - - +
138D ALA* 6.1 0.2 - - - -
747D HEM 5.9 0.2 - - - -
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Residues in contact with ASN 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PHE* 5.7 0.5 - - - -
103C HIS* 3.4 48.3 + - + +
35D TYR* 5.3 6.7 + - - +
104D ARG* 2.9 53.9 + - - +
105D LEU* 3.8 7.7 - - - +
107D GLY* 1.3 74.6 - - - +
109D VAL* 1.3 64.9 + - - +
111D VAL* 3.3 2.0 + - - -
112D CYS* 3.0 21.7 + - - -
131D GLN* 3.8 13.0 + - - -
134D VAL* 5.0 2.4 - - - +
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Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C HIS* 4.7 10.5 - - + -
27D ALA* 3.3 31.9 - - - +
30D ARG* 3.5 24.2 - - + +
31D LEU* 4.0 14.1 - - + +
34D VAL* 5.2 0.4 - - + -
35D TYR* 3.7 23.8 - - + +
105D LEU 3.0 21.0 + - - +
106D LEU* 3.6 9.0 - - + +
108D ASN* 1.3 72.8 - - + +
110D LEU* 1.3 61.0 + - - +
112D CYS* 3.0 8.9 + - - +
113D VAL* 2.8 28.6 + - + +
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TRP* 4.5 13.2 - - + -
23D VAL* 4.1 17.5 - - + -
27D ALA* 4.2 14.8 - - + +
68D LEU* 4.0 22.0 - - + -
71D PHE* 3.8 46.7 - - + -
106D LEU* 2.9 14.7 + - + +
107D GLY* 3.5 9.0 - - - +
108D ASN 3.3 0.2 - - - -
109D VAL* 1.3 77.4 - - - +
111D VAL* 1.3 57.6 + - - +
113D VAL* 3.1 4.4 + - + +
114D LEU* 2.9 47.7 + - + +
130D TYR* 6.0 1.1 - - + -
134D VAL* 4.5 8.7 - - + -
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Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C HIS* 3.9 2.9 - - + +
107C VAL* 3.9 15.7 - - + -
107D GLY 3.0 18.8 + - - +
108D ASN* 3.5 7.6 - - - +
109D VAL 3.2 0.4 - - - -
110D LEU* 1.3 76.6 - - - +
112D CYS* 1.3 61.0 + - - +
114D LEU* 3.4 11.2 + - + +
115D ALA* 3.1 21.1 + - - +
122D PHE* 3.8 22.4 - - + -
127D GLN* 4.2 2.7 - - + -
130D TYR* 4.7 11.7 - - + -
131D GLN* 3.5 28.7 - - - +
134D VAL* 4.0 25.1 - - + -
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Residues in contact with CYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C HIS* 4.1 7.2 - - - -
106C LEU* 4.0 28.7 - - - -
107C VAL* 4.1 18.4 - - - -
110C ALA* 3.6 5.6 - - + +
117C PHE* 4.6 8.7 - - + -
122C HIS* 4.1 26.7 - - + -
30D ARG* 5.7 1.1 - - - -
108D ASN 3.0 18.1 + - - -
109D VAL* 3.0 8.0 + - - +
111D VAL* 1.3 77.6 - - - +
113D VAL* 1.3 57.8 + - + +
115D ALA* 3.3 7.1 + - - +
116D ARG* 2.9 28.6 + - - +
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 3.7 30.1 - - + +
26D GLU* 3.7 18.4 - - + +
27D ALA* 3.8 22.2 - - + -
30D ARG* 3.7 27.4 - - - +
109D VAL* 2.8 18.6 + - + +
110D LEU* 3.5 9.4 - - - +
112D CYS* 1.3 74.1 - - - +
114D LEU* 1.3 64.9 + - - +
116D ARG* 3.3 1.8 + - - +
117D ASN* 2.8 46.6 + - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 4.9 2.2 - - + -
15D TRP* 4.5 8.7 - - + -
18D VAL* 4.1 16.2 - - + -
23D VAL* 4.5 16.8 - - + -
110D LEU* 2.9 34.8 + - + +
111D VAL* 3.7 6.3 - - + +
112D CYS 3.3 0.2 - - - -
113D VAL* 1.3 75.0 - - - +
115D ALA* 1.3 58.6 + - - +
117D ASN* 4.8 0.7 - - - -
118D PHE* 2.9 58.1 + - + +
122D PHE* 3.7 24.9 - - + -
130D TYR* 3.7 38.1 - - + -
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C VAL* 3.6 31.2 - - + +
110C ALA* 4.1 1.8 - - + -
111C ALA* 3.4 11.7 - - + +
111D VAL 3.1 13.6 + - - +
112D CYS 3.5 8.5 - - - +
114D LEU* 1.3 77.6 - - - +
116D ARG* 1.3 57.3 + - - +
119D GLY* 2.8 30.8 + - - -
122D PHE* 3.7 26.4 - - + -
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ALA* 3.4 26.9 - - + +
114C PRO* 3.0 58.0 + - + +
115C ALA* 5.1 0.2 - - - +
117C PHE* 3.6 9.0 - - + -
26D GLU* 2.7 38.4 + - - +
30D ARG* 3.3 24.7 - - - +
112D CYS 2.9 16.9 + - - +
113D VAL* 3.7 5.2 - - - +
115D ALA* 1.3 77.3 - - - +
117D ASN* 1.3 73.1 + - - +
119D GLY* 4.2 2.6 + - - -
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Residues in contact with ASN 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ALA* 5.5 5.7 - - - +
23D VAL* 4.3 16.8 - - + +
26D GLU* 3.1 26.9 + - - +
113D VAL* 2.8 36.0 + - - +
114D LEU* 4.1 2.5 - - - +
116D ARG* 1.3 92.4 + - - +
118D PHE* 1.3 73.8 + - + +
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Residues in contact with PHE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.5 55.9 - - + -
17D LYS* 3.9 30.3 - - + -
18D VAL* 3.8 24.7 - - + -
23D VAL* 5.6 2.2 - - + -
114D LEU* 2.9 36.6 + - + +
117D ASN* 1.3 87.6 - - + +
119D GLY* 1.3 65.6 + - - +
120D LYS 3.4 0.5 + - - -
121D GLU* 3.2 34.3 + - + +
122D PHE* 4.3 8.1 - - + -
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Residues in contact with GLY 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ALA* 3.5 27.6 - - - +
114C PRO* 5.8 2.5 - - - -
115D ALA 2.8 17.4 + - - -
116D ARG 4.2 3.0 + - - -
117D ASN 3.7 1.4 - - - -
118D PHE* 1.3 75.8 - - - +
120D LYS* 1.3 53.8 + - - -
122D PHE* 2.8 34.8 + - - +
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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