Contacts of the helix formed by residues 108 - 120 (chain D) in PDB entry 1H48
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 HIS 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C PRO* 3.2 47.7 - - + +
108C HIS* 3.9 13.9 + + - -
23D VAL* 3.8 24.6 - - + +
24D ARG 4.8 0.2 - - - -
25D ILE* 3.7 43.2 - - + +
26D PRO* 4.6 1.1 - - + +
104D LYS 3.4 24.9 + - - -
105D MET 2.8 7.2 + - - +
107D PRO* 1.3 80.5 - - + +
109D ILE* 1.3 63.9 + - - +
110D PRO* 3.4 2.7 - - - -
111D GLN* 3.2 12.0 + - - +
112D MET* 3.1 25.9 + - + +
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Residues in contact with ILE 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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98D ILE* 5.0 0.4 - - + -
105D MET* 3.3 11.4 + - + +
106D LEU* 3.4 37.2 + - + +
108D HIS* 1.3 77.9 - - - +
110D PRO* 1.3 66.3 - - + +
112D MET* 3.1 13.8 + - + +
113D ARG* 3.0 39.2 + - - +
129D VAL* 3.6 46.0 - - + +
130D LYS* 4.0 20.6 - - - +
131D ALA* 4.1 7.4 - - + +
56F ASP* 4.9 0.4 - - - +
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Residues in contact with PRO 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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17C PRO* 5.2 2.9 - - + -
24C ARG* 3.7 32.0 - - + +
26C PRO* 3.9 27.6 - - + -
106D LEU 3.6 10.3 - - - +
107D PRO 3.8 5.6 - - - +
108D HIS 3.5 3.4 - - - -
109D ILE* 1.3 95.9 - - + +
111D GLN* 1.3 61.8 + - - +
113D ARG* 3.3 12.0 + - + +
114D VAL* 3.1 25.3 + - - +
124D MET* 4.4 1.6 - - + +
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Residues in contact with GLN 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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22C GLY 3.8 4.1 + - - +
23C VAL* 3.6 16.3 - - + -
24C ARG* 2.9 44.6 + - - +
111C GLN* 4.6 7.0 - - + -
115C PHE* 3.9 12.1 - - - -
23D VAL* 3.7 20.9 - - + -
108D HIS* 3.2 11.8 + - - +
110D PRO* 1.3 79.7 - - - +
112D MET* 1.3 60.6 + - - +
114D VAL* 3.2 17.5 + - - +
115D PHE* 3.0 57.6 + - + -
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Residues in contact with MET 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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20D ILE* 3.4 46.2 - - + +
21D GLY* 3.5 24.7 - - - +
23D VAL* 3.8 4.0 - - + -
25D ILE* 4.1 5.8 - - + -
40D ALA* 5.6 0.4 - - - -
98D ILE* 3.8 23.1 - - + -
105D MET* 4.4 8.3 - - - +
108D HIS* 3.1 37.3 + - + +
109D ILE* 3.1 12.5 + - + +
111D GLN* 1.3 75.1 - - - +
113D ARG* 1.3 58.8 + - - +
115D PHE* 3.2 2.6 + - - +
116D ILE* 2.8 35.6 + - + +
129D VAL* 4.0 20.6 - - + -
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Residues in contact with ARG 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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109D ILE* 3.0 31.4 + - + +
110D PRO* 3.6 10.9 - - - +
111D GLN 3.3 0.2 - - - -
112D MET* 1.3 75.0 - - - +
114D VAL* 1.3 58.0 + - - +
116D ILE* 4.1 0.8 - - - +
117D ALA* 2.9 32.1 + - - +
124D MET* 2.9 58.4 + - + +
125D ASP* 4.2 5.5 + - - +
127D VAL* 2.7 34.8 + - + +
128D ASN* 4.3 4.1 - - - +
129D VAL* 4.2 21.3 - - + +
53F ALA* 4.1 23.9 + - - +
59F LYS* 5.6 6.3 - - - +
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Residues in contact with VAL 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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24C ARG* 3.5 35.0 - - + +
110D PRO 3.1 15.9 + - - +
111D GLN* 3.5 22.2 - - - +
112D MET 3.2 0.2 - - - -
113D ARG* 1.3 74.4 - - - +
115D PHE* 1.3 67.3 + - + +
117D ALA* 3.9 1.1 - - - +
118D GLU* 3.0 50.9 + - + +
124D MET* 3.9 14.6 - - + -
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Residues in contact with PHE 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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74C ARG* 5.8 0.4 - - - -
111C GLN* 3.9 8.1 - - - -
115C PHE* 3.5 30.5 - + - -
21D GLY 3.5 21.8 - - - +
22D GLY* 3.3 29.4 - - - -
23D VAL* 3.8 13.7 - - + -
41D LEU* 6.3 0.7 - - + -
74D ARG* 3.4 40.2 - - + +
111D GLN* 3.0 37.7 + - + -
112D MET 3.5 6.5 - - - +
114D VAL* 1.3 78.6 - - + +
116D ILE* 1.3 58.3 + - + +
118D GLU* 3.4 9.1 + - - +
119D ASP* 2.9 36.4 + - - +
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Residues in contact with ILE 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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21D GLY* 4.9 3.8 - - - +
40D ALA* 6.3 0.9 - - + -
41D LEU* 3.7 31.2 - - + -
44D LEU* 3.8 24.2 - - + -
77D LEU* 4.8 2.5 - - + -
94D VAL* 4.4 2.2 - - + -
96D VAL* 4.9 7.4 - - + -
112D MET* 2.8 29.3 + - + +
115D PHE* 1.3 74.0 - - + +
117D ALA* 1.3 63.1 + - - +
119D ASP* 3.3 5.5 + - - +
120D LEU* 3.1 34.1 + - + +
127D VAL* 3.7 27.1 - - + -
129D VAL* 3.9 26.9 - - + -
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Residues in contact with ALA 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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113D ARG 2.9 19.1 + - - +
114D VAL* 3.9 2.5 - - - +
116D ILE* 1.3 78.6 - - - +
118D GLU* 1.4 62.5 + - + +
120D LEU 3.3 1.0 + - - -
121D GLY 3.0 4.0 + - - -
122D CYS* 2.8 57.3 + - - +
123D HIS 4.1 1.3 - - - -
124D MET* 3.8 25.8 - - + +
127D VAL* 4.1 3.1 - - + -
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Residues in contact with GLU 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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74D ARG* 4.4 10.6 + - - +
78D ARG* 5.7 0.3 - - - -
114D VAL* 3.0 42.4 + - + +
115D PHE* 3.7 8.3 - - - +
117D ALA* 1.4 76.2 - - + +
119D ASP* 1.3 61.8 + - - +
121D GLY* 3.1 19.1 + - - +
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Residues in contact with ASP 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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41D LEU* 5.1 0.2 - - - +
74D ARG* 2.7 50.8 + - - +
77D LEU* 4.0 19.7 - - + +
78D ARG* 2.8 54.6 + - + +
81D TRP* 3.7 12.3 - - - -
115D PHE* 2.9 22.4 + - - +
116D ILE* 3.3 4.0 + - - +
118D GLU* 1.3 73.7 - - - +
120D LEU* 1.3 61.1 + - - +
121D GLY 3.5 0.2 - - - -
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Residues in contact with LEU 120 (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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44D LEU* 4.7 2.0 - - + -
48D LEU* 4.1 14.6 - - + -
77D LEU* 3.9 22.7 - - + -
81D TRP* 3.1 59.8 + - + +
91D LEU* 4.0 30.3 - - + +
94D VAL* 4.4 9.0 - - + -
116D ILE* 3.1 36.6 + - + +
117D ALA 4.1 1.6 - - - +
118D GLU 3.1 0.2 - - - -
119D ASP* 1.3 79.7 - - - +
121D GLY* 1.3 64.6 - - - +
122D CYS* 3.3 13.2 + - - +
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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
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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