Contacts of the helix formed by residues 123 - 140 (chain A) in PDB entry 1HH1
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A VAL* 5.3 5.6 - - + -
97A LEU 3.7 4.7 - - - +
98A LYS* 2.8 27.6 + - - +
99A PHE* 4.0 2.9 - - - -
122A LEU* 1.3 78.7 - - - +
124A LEU* 1.3 65.2 + - - +
125A GLU* 3.4 10.5 + - - +
126A ASP* 2.9 49.2 + - - +
127A LEU* 3.2 14.9 + - - +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ILE* 5.0 6.7 - - + +
18A ARG* 3.6 52.9 - - + +
19A LEU* 4.0 26.0 - - + -
22A LYS* 3.7 26.0 - - + -
97A LEU* 4.5 6.4 + - + +
99A PHE* 3.8 33.2 - - + -
123A ASP* 1.3 73.1 - - - +
125A GLU* 1.3 64.5 + - - +
127A LEU* 3.2 9.6 + - + +
128A VAL* 2.9 31.0 + - + +
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 4.8 15.1 + - - +
123A ASP* 3.4 11.4 + - - +
124A LEU* 1.3 77.6 - - - +
126A ASP* 1.3 59.0 + - - +
128A VAL* 3.4 10.5 + - - +
129A ARG* 2.7 72.5 + - - +
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Residues in contact with ASP 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLY 4.9 0.9 - - - +
122A LEU* 3.6 25.2 - - + +
123A ASP* 2.9 45.3 + - - +
125A GLU* 1.3 75.2 - - - +
127A LEU* 1.3 58.6 + - - +
129A ARG* 3.3 12.1 + - - +
130A LEU* 3.0 30.8 + - - +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 5.5 0.7 - - + -
52A ILE* 4.2 19.3 - - + -
54A ILE* 4.0 20.4 - - + -
88A PHE* 3.7 43.7 - - + -
99A PHE* 3.6 38.6 - - + -
122A LEU* 4.0 11.6 - - + +
123A ASP 3.2 10.0 + - - +
124A LEU* 3.4 16.4 - - + +
126A ASP* 1.3 73.5 - - - +
128A VAL* 1.3 67.8 + - + +
130A LEU* 2.9 16.9 + - + +
131A VAL* 3.1 13.0 + - - +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.1 13.7 - - + -
22A LYS* 4.0 29.8 - - + -
24A PHE* 3.9 30.1 - - + -
124A LEU* 2.9 25.0 + - + +
125A GLU* 3.8 12.1 - - - +
127A LEU* 1.3 74.1 - - + +
129A ARG* 1.3 51.5 + - + +
131A VAL* 3.0 11.7 + - - +
132A GLU* 2.7 55.1 + - + +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLU* 2.7 55.0 + - - +
126A ASP* 3.6 12.1 - - - +
127A LEU 3.2 0.4 - - - -
128A VAL* 1.3 73.1 - - + +
130A LEU* 1.3 65.6 + - - +
132A GLU* 3.9 9.9 - - + +
133A ALA* 2.8 25.3 + - - +
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 4.1 20.9 - - + -
101A PRO* 6.0 1.1 - - + -
122A LEU* 3.5 32.1 - - + -
126A ASP 3.0 17.7 + - - +
127A LEU* 2.9 9.8 + - + +
129A ARG* 1.3 76.3 - - - +
131A VAL* 1.3 65.5 + - + +
133A ALA* 3.4 5.3 + - + +
134A LYS* 3.1 38.6 + - + +
137A ARG* 4.3 2.4 + - - +
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.8 35.4 - - + -
47A LYS* 4.2 5.8 - - + +
50A VAL* 4.0 23.3 - - + +
52A ILE* 3.5 35.0 - - + -
127A LEU* 3.1 10.7 + - + +
128A VAL* 3.0 7.9 + - - +
130A LEU* 1.3 78.6 - - + +
132A GLU* 1.3 64.8 + - + +
134A LYS* 3.1 6.3 + - + +
135A ILE* 3.0 37.5 + - + +
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 2.8 35.1 + - - -
128A VAL* 2.7 40.7 + - + +
129A ARG* 3.3 10.5 + - + +
131A VAL* 1.3 72.8 - - + +
133A ALA* 1.3 61.4 + - - +
135A ILE* 3.4 22.0 + - - +
136A SER* 3.1 24.8 + - - -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ARG 2.8 20.4 + - - +
130A LEU* 3.9 4.0 - - + +
131A VAL 3.2 0.2 - - - -
132A GLU* 1.3 70.6 - - - +
134A LYS* 1.3 66.0 + - - +
136A SER* 3.3 8.3 + - - -
137A ARG* 3.1 41.7 + - - +
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A VAL* 3.9 29.8 - - + +
52A ILE* 5.7 1.6 - - + +
86A SER* 2.8 32.7 + - - -
88A PHE* 5.9 1.4 - - - -
130A LEU* 3.1 26.1 + - + +
131A VAL* 3.1 6.5 + - + +
133A ALA* 1.3 77.4 - - - +
135A ILE* 1.3 63.4 + - - +
137A ARG* 3.3 34.5 + - - +
138A THR* 3.2 25.8 + - - +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.6 33.7 - - + +
48A ASN* 3.7 37.9 - - + +
50A VAL* 3.7 15.9 - - + -
131A VAL* 3.0 24.1 + - + +
132A GLU* 3.6 27.4 - - - +
133A ALA 3.3 0.2 - - - -
134A LYS* 1.3 75.9 - - - +
136A SER* 1.3 58.4 + - - +
138A THR* 3.1 8.9 + - - -
139A LEU* 2.9 43.0 + - + +
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLU 3.1 13.0 + - - -
133A ALA* 3.6 11.2 - - - -
134A LYS 3.3 0.4 - - - -
135A ILE* 1.3 80.2 - - - +
137A ARG* 1.3 56.3 + - - +
139A LEU* 3.4 10.1 + - - +
140A ASP* 2.9 40.7 + - - +
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 4.3 2.6 + - - +
133A ALA* 3.1 28.9 + - - +
134A LYS* 3.3 52.6 + - - +
136A SER* 1.3 75.9 - - - +
138A THR* 1.3 62.4 + - - +
140A ASP* 3.3 21.9 - - - +
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASN 5.9 3.6 - - - +
50A VAL* 5.7 2.4 - - - +
134A LYS* 3.2 11.7 + - - +
135A ILE* 3.1 10.8 + - - -
137A ARG* 1.3 80.1 - - - +
139A LEU* 1.3 66.9 + - + +
140A ASP 3.5 5.2 + - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASN* 4.4 21.1 - - - +
135A ILE* 2.9 33.0 + - + +
136A SER* 3.8 7.2 - - - +
138A THR* 1.3 80.5 - - + +
140A ASP* 1.3 73.2 + - - +
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER* 2.9 23.7 + - - +
137A ARG* 3.3 17.6 - - - +
138A THR 3.5 4.7 - - - +
139A LEU* 1.3 92.5 - - - +
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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