Contacts of the helix formed by residues 129 - 140 (chain B) in PDB entry 1HNB
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 ALA 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B GLN* 5.1 13.9 + - - +
125B GLU 2.9 14.7 + - - +
126B TYR* 3.1 9.5 + - - +
128B GLN* 1.3 75.8 - - - +
130B LEU* 1.3 63.7 + - - +
131B PRO* 3.6 0.9 - - - -
132B GLU* 3.5 28.8 - - - +
133B MET* 4.0 12.6 + - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TYR* 2.8 31.4 + - + +
127B LEU* 3.4 11.7 - - + +
129B ALA* 1.3 77.0 - - - +
131B PRO* 1.3 70.3 - - + +
132B GLU 3.0 0.9 + - - -
133B MET* 3.0 18.7 + - + +
134B LEU* 2.8 50.5 + - + +
166B ASN* 3.5 23.6 - - + +
169B PHE* 3.9 31.6 - - + -
170B GLU* 4.9 0.4 - - + -
173B CYS* 4.0 22.4 - - + -
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Residues in contact with PRO 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU 3.2 14.6 - - - +
128B GLN 3.9 8.5 - - - +
129B ALA 3.8 1.8 - - - -
130B LEU* 1.3 92.1 - - + +
132B GLU* 1.3 53.7 + - + +
134B LEU* 4.2 9.6 - - + -
135B LYS* 2.7 37.1 + - - +
173B CYS 5.7 2.2 - - - +
177B PHE* 3.8 15.8 - - + -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE* 5.9 2.4 - - - -
128B GLN 4.9 3.8 - - - +
129B ALA* 3.5 34.1 - - - +
130B LEU 3.0 0.8 + - - -
131B PRO* 1.3 80.5 - - + +
133B MET* 1.3 65.0 + - - +
135B LYS* 3.6 3.8 - - - +
136B LEU* 2.9 31.4 + - + +
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Residues in contact with MET 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B SER* 3.5 32.5 - - - +
109B GLN* 3.6 18.8 - - - +
126B TYR* 3.2 12.6 - - - +
129B ALA 4.0 8.2 + - - +
130B LEU* 3.0 19.2 + - + +
132B GLU* 1.3 78.6 - - - +
134B LEU* 1.3 70.5 + - + +
136B LEU* 2.9 27.6 + - - +
137B TYR* 3.2 35.8 + - + -
162B VAL* 4.8 2.5 - - + -
163B LEU* 6.2 0.4 - - + -
166B ASN* 3.2 31.2 - - - +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 2.8 52.3 + - + +
131B PRO* 4.0 2.5 - - + +
133B MET* 1.3 80.8 - - + +
135B LYS* 1.3 60.8 + - - +
137B TYR* 3.7 5.9 + - + +
138B SER* 3.3 8.7 + - - -
163B LEU* 4.1 19.5 - - + -
166B ASN* 5.2 4.5 - - + -
173B CYS* 3.9 36.3 - - + +
174B LEU* 4.5 11.4 - - + -
177B PHE* 3.5 18.1 - - + -
180B LEU* 3.2 37.6 - - + +
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PRO 2.7 23.4 + - - +
132B GLU* 3.6 4.5 - - - +
134B LEU* 1.3 70.9 - - - +
136B LEU* 1.3 68.7 + - + +
137B TYR 3.1 0.2 - - - -
138B SER* 2.7 26.1 + - - +
139B GLN* 2.8 40.6 + - + +
177B PHE* 3.8 15.9 - - + -
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE* 5.7 7.6 - - + -
55A ASP 4.0 17.4 - - - +
56A PHE* 3.8 29.8 - - + -
57A PRO* 4.6 12.8 - - + +
102B GLN* 5.5 4.5 - - - +
132B GLU* 2.9 24.3 + - + +
133B MET* 2.9 17.8 + - - +
135B LYS* 1.3 77.3 - - + +
137B TYR* 1.3 62.9 + - - +
139B GLN* 3.3 23.1 + - - +
140B PHE* 3.1 21.8 + - - +
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A PHE* 3.9 25.8 - + - -
99B LEU* 4.2 6.5 - - + -
102B GLN* 4.0 7.8 - - + +
103B PHE* 3.2 60.3 + + - -
106B SER* 3.0 23.4 + - - -
133B MET* 3.2 43.8 + - + -
134B LEU* 3.9 9.9 - - + +
135B LYS 3.1 0.6 - - - -
136B LEU* 1.3 74.7 - - - +
138B SER* 1.3 58.1 + - - +
140B PHE* 2.7 30.8 + - - +
141B LEU* 3.3 8.5 + - - +
147B PHE* 4.3 9.7 - + + -
162B VAL* 5.4 1.8 - - + -
163B LEU* 4.4 14.1 - - + -
180B LEU* 4.0 16.2 - - + -
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU 3.3 9.5 + - - -
135B LYS* 2.7 31.9 + - - +
137B TYR* 1.3 77.5 - - - +
139B GLN* 1.3 56.7 + - - +
141B LEU* 4.8 0.7 - - - -
142B GLY* 3.1 14.0 + - - -
177B PHE* 3.6 15.1 - - - -
179B ASN* 3.0 43.0 + - - +
180B LEU* 3.9 13.1 - - - +
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Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASP 5.3 2.8 + - - -
135B LYS* 2.8 42.3 + - + +
136B LEU* 3.5 35.2 + - - +
138B SER* 1.3 76.5 + - - +
140B PHE* 1.3 58.1 + - - +
141B LEU 3.2 5.9 + - - -
142B GLY* 4.3 4.2 + - - -
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Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASP* 3.3 39.9 - - + +
56A PHE* 3.5 23.8 - + + -
94B ILE* 6.6 0.2 - - + -
95B ARG* 3.2 62.9 + - + +
98B ILE* 4.8 11.0 - - + -
99B LEU* 3.5 41.5 - - + -
136B LEU 3.1 11.6 + - - +
137B TYR* 2.7 10.4 + - - +
139B GLN* 1.3 77.1 - - - +
141B LEU* 1.3 58.7 + - - +
144B GLN* 4.9 0.2 - - - -
147B PHE* 4.0 7.2 - + + -
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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