Contacts of the helix formed by residues 113 - 132 (chain B) in PDB entry 1HYH
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 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 3.3 40.6 - - + +
103B GLN* 3.8 16.1 - - - +
112B PHE* 1.3 76.2 - - - +
114B GLU* 1.3 60.9 + - - +
115B LEU 3.5 0.5 + - - -
116B LYS* 4.2 5.4 + - - -
117B PHE 5.0 0.5 + - - -
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Residues in contact with GLU 114 (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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98B GLY* 3.8 1.9 - - - -
99B ASN 2.9 46.0 + - - +
100B ILE* 4.2 1.7 - - - +
102B LEU* 3.8 18.2 - - + -
103B GLN* 3.7 32.0 + - - +
112B PHE 3.3 1.2 - - - -
113B ALA* 1.3 73.2 - - - +
115B LEU* 1.3 57.9 + - - +
116B LYS 3.2 1.3 - - - -
117B PHE* 3.0 5.6 + - + -
118B THR* 2.7 44.1 + - + +
143B ASN* 4.0 8.7 - - + +
330B NAD 2.8 40.9 + - - -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.0 44.6 + - + +
114B GLU* 1.3 75.4 - - - +
116B LYS* 1.3 57.5 + - - +
118B THR* 3.7 4.7 - - - -
119B SER* 2.5 56.8 + - - +
144B PRO* 3.6 28.8 - - + +
147B VAL* 4.2 13.7 - - + -
148B ILE* 3.9 9.2 - - + -
321B ARG* 5.0 14.6 - - + +
324B GLU* 5.1 6.5 - - - +
325B ILE* 4.5 15.9 - - + -
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA 4.2 5.3 + - - -
114B GLU 3.2 0.8 - - - -
115B LEU* 1.3 80.8 - - - +
117B PHE* 1.3 61.9 + - - +
119B SER* 3.7 4.6 - - - -
120B SER* 3.3 21.5 + - - -
325B ILE* 5.4 5.4 - - - -
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Residues in contact with PHE 117 (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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98B GLY* 3.6 36.1 - - - -
99B ASN* 4.0 18.8 - - + -
102B LEU* 3.6 23.2 - - + +
113B ALA 5.0 0.4 + - - -
114B GLU 3.0 8.0 + - - +
116B LYS* 1.3 71.6 - - - +
118B THR* 1.3 72.7 + - + +
120B SER* 3.1 24.3 + - - -
121B MET* 3.4 45.7 - - + +
330B NAD 4.0 17.7 - + - -
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.2 13.0 - - + +
98B GLY* 3.7 28.9 - - - -
114B GLU* 2.7 34.0 + - + +
115B LEU* 3.7 1.7 - - - -
117B PHE* 1.3 77.6 - - + +
119B SER* 1.3 60.6 + - - +
120B SER 3.3 0.7 + - - -
121B MET* 3.3 15.2 + - - +
122B VAL* 3.4 16.1 + - - +
142B SER* 4.9 3.1 - - - -
143B ASN 3.0 27.5 + - - +
148B ILE* 3.5 20.4 - - - +
330B NAD 4.3 1.3 - - - +
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 2.5 43.2 + - - +
116B LYS* 3.7 4.5 - - - -
118B THR* 1.3 75.3 + - - +
120B SER* 1.3 62.0 + - - +
121B MET 3.5 0.2 + - - -
122B VAL* 3.6 15.9 + - - +
123B GLN* 4.2 4.0 + - - +
148B ILE* 4.0 8.1 - - - +
151B LEU* 4.1 7.1 - - - +
325B ILE* 3.5 25.8 - - - +
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS 3.3 13.3 + - - -
117B PHE* 3.1 13.1 + - - -
119B SER* 1.3 79.2 - - - +
121B MET* 1.3 76.6 + - - +
122B VAL 3.6 0.2 + - - -
123B GLN* 3.8 12.0 + - - +
124B SER* 4.2 5.7 + - - -
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Residues in contact with MET 121 (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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97B LEU* 3.8 19.3 - - + -
117B PHE* 3.4 60.6 - - + +
118B THR 3.6 7.4 - - - +
119B SER 3.3 0.2 - - - -
120B SER* 1.3 90.2 - - - +
122B VAL* 1.3 65.9 + - - +
124B SER* 3.2 9.0 + - - -
125B VAL* 3.0 26.9 + - - +
330B NAD 3.4 33.9 - - - +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 5.7 2.2 - - + -
118B THR 3.4 15.7 + - - +
119B SER* 3.8 13.0 - - - +
120B SER 3.4 0.4 - - - -
121B MET* 1.3 77.6 - - + +
123B GLN* 1.3 59.0 + - - +
126B GLY* 2.8 28.6 + - - -
148B ILE* 3.7 28.9 - - + -
151B LEU* 3.7 33.7 - - + +
152B PHE* 4.0 25.5 - - + +
155B VAL* 3.8 17.3 - - + +
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Residues in contact with GLN 123 (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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119B SER 4.2 3.7 + - - +
120B SER 3.8 9.2 + - - +
121B MET 3.3 1.4 + - - -
122B VAL* 1.3 77.6 - - - +
124B SER* 1.3 58.7 + - - +
127B THR* 2.9 55.9 + - - +
155B VAL* 3.6 28.2 - - + +
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER 4.2 5.2 + - - -
121B MET* 3.2 14.2 + - - -
123B GLN* 1.3 76.9 - - - +
125B VAL* 1.3 69.0 + - - +
127B THR* 3.3 4.9 + - - -
128B ASN* 2.9 39.3 + - - +
330B NAD 5.2 2.9 + - - -
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 4.2 15.9 - - + -
84B TRP* 3.7 24.3 - - + -
97B LEU* 3.6 26.7 - - + -
121B MET 3.0 19.9 + - - +
122B VAL 4.2 0.7 - - - +
124B SER* 1.3 79.0 - - - +
126B GLY* 1.3 64.2 + - - +
128B ASN* 3.6 3.6 - - - +
129B LEU* 3.0 25.2 + - + +
152B PHE* 3.7 24.9 - - + -
330B NAD 3.7 22.7 - - - +
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Residues in contact with GLY 126 (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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122B VAL 2.8 19.2 + - - -
123B GLN 3.9 0.4 - - - -
125B VAL* 1.3 77.6 - - - +
127B THR* 1.3 54.8 + - - +
129B LEU* 3.5 2.0 - - - +
130B LYS* 2.8 30.8 + - - +
152B PHE* 4.1 10.5 - - - -
155B VAL* 4.3 8.3 - - - -
156B THR* 3.3 25.5 - - - +
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLN* 2.9 39.4 + - - +
124B SER* 3.7 6.5 - - - +
126B GLY* 1.3 75.1 - - - +
128B ASN* 1.3 58.3 + - - +
130B LYS* 3.2 12.5 + - + +
131B GLU* 2.9 50.2 + - + +
155B VAL* 4.3 5.0 + - - +
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Residues in contact with ASN 128 (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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84B TRP* 3.6 45.6 + - + +
124B SER* 2.9 33.2 + - - +
125B VAL* 3.6 3.8 - - - +
127B THR* 1.3 79.0 - - - +
129B LEU* 1.3 57.6 + - - +
131B GLU* 3.5 14.1 + - - +
132B SER* 3.1 27.5 + - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 4.4 6.3 - - + -
84B TRP* 3.7 9.6 - - + -
87B LEU* 3.5 30.3 - - + -
93B VAL* 4.2 12.8 - - + -
125B VAL 3.0 18.2 + - - +
126B GLY 3.5 4.7 - - - +
128B ASN* 1.3 72.5 - - - +
130B LYS* 1.3 67.2 + - - +
132B SER* 2.5 25.5 + - - +
134B PHE* 4.0 23.9 + - + +
138B LEU* 3.7 33.7 - - + -
152B PHE* 5.1 6.5 - - + -
156B THR* 4.7 4.5 - - + -
158B PHE* 4.2 18.0 - - + -
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Residues in contact with LYS 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 GLY 2.8 18.9 + - - +
127B THR* 3.3 11.7 - - + +
129B LEU* 1.3 77.7 - - - +
131B GLU* 1.3 62.1 + - + +
132B SER 3.5 0.2 + - - -
133B GLY* 3.8 9.9 + - - -
134B PHE 4.9 0.9 + - - +
155B VAL 4.8 4.0 - - - +
156B THR* 3.3 33.9 - - - +
158B PHE* 4.0 19.3 - - + -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B THR* 2.9 35.9 + - + +
128B ASN* 3.7 14.8 - - - +
130B LYS* 1.3 75.6 - - + +
132B SER* 1.3 61.3 + - - +
133B GLY* 3.2 3.3 + - - -
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TRP* 3.2 33.4 - - - -
85B ALA* 4.3 7.4 - - - +
87B LEU* 4.1 6.8 - - - +
88B ALA* 3.6 18.8 + - - +
128B ASN 3.1 12.3 + - - -
129B LEU* 2.5 25.7 + - - +
131B GLU* 1.3 77.1 - - - +
133B GLY* 1.3 56.5 + - - +
134B PHE* 3.2 17.3 + - - +
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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
------------------------------------------------------------
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