Contacts of the helix formed by residues 126 - 138 (chain B) in PDB entry 2HYE
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 SER 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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886A SER* 5.4 4.9 - - - -
909A ILE* 4.3 4.0 - - - +
111B THR* 4.2 13.6 - - - +
113B THR* 3.5 5.8 + - - -
125B GLY* 1.3 75.0 - - - -
127B TYR* 1.3 66.4 + - - +
128B LYS* 3.8 2.8 + - - +
129B GLY* 2.8 21.0 + - - -
130B VAL* 3.1 23.2 + - - +
188B GLU* 3.1 20.3 + - - -
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Residues in contact with TYR 127 (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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841A ALA* 4.2 11.8 + - + -
842A GLU* 3.4 23.1 - - + +
886A SER* 5.2 4.0 + - - +
909A ILE* 3.6 32.7 + - + +
910A MET* 4.6 11.7 - - + -
926A LEU* 4.4 24.0 - - + -
927A MET* 6.4 0.9 - - - -
21B LEU 5.2 0.7 + - - -
23B THR* 3.4 29.8 - - + +
26B TYR* 4.3 12.1 - + - -
38B LEU* 5.2 3.1 - - + -
44B PRO* 5.1 5.3 - - + +
126B SER* 1.3 68.5 - - - +
128B LYS* 1.3 89.0 + - + +
130B VAL* 3.0 16.0 + - + +
131B LYS* 3.0 51.3 + - + +
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Residues in contact with LYS 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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841A ALA* 4.0 15.9 - - + -
842A GLU* 3.3 36.6 + - - +
44B PRO* 6.0 4.0 - - + -
47B VAL* 5.1 4.3 - - + -
126B SER* 3.8 4.1 + - - +
127B TYR* 1.3 94.8 - - + +
129B GLY* 1.3 67.7 + - - +
131B LYS* 3.2 7.3 + - - +
132B LEU* 3.1 29.2 + - + +
146B GLU* 3.0 40.9 + - - +
173B ARG* 6.1 0.2 - - - +
175B TYR* 3.8 20.0 + - + +
188B GLU* 4.6 1.3 - - - +
217B GLU* 4.1 15.8 + - - -
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Residues in contact with GLY 129 (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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113B THR* 3.6 17.3 - - - -
126B SER* 2.8 23.2 + - - -
128B LYS* 1.3 80.9 - - - +
130B VAL* 1.3 61.7 + - - +
132B LEU* 3.3 2.8 + - - +
133B ALA* 2.9 21.0 + - - +
175B TYR* 4.8 2.0 - - - -
186B VAL* 4.0 10.3 - - - +
188B GLU* 3.5 12.9 + - - -
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Residues in contact with VAL 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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909A ILE* 4.3 22.7 - - + -
927A MET* 3.9 28.7 - - + -
113B THR* 3.3 17.4 - - + +
114B VAL 4.7 1.6 - - - +
115B LEU* 3.9 20.3 - - + +
123B PRO* 4.6 10.8 - - + -
124B SER 4.5 1.8 - - - +
126B SER 3.1 14.1 + - - +
127B TYR* 3.0 7.5 + - + +
129B GLY* 1.3 73.6 - - - +
131B LYS* 1.3 64.9 + - - +
133B ALA* 3.1 8.2 + - - +
134B LYS* 3.1 22.2 + - + +
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Residues in contact with LYS 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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26B TYR* 4.5 8.1 - - - -
38B LEU* 2.8 52.5 - - - +
42B THR* 4.6 12.8 - - - +
44B PRO* 3.9 34.5 - - + -
127B TYR* 3.0 42.5 + - + +
128B LYS* 3.5 12.8 - - - +
130B VAL* 1.3 78.9 - - - +
132B LEU* 1.3 63.9 + - - +
134B LYS* 3.2 5.2 + - - +
135B PHE* 3.0 20.3 + - + +
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Residues in contact with LEU 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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43B ILE* 3.6 31.2 - - + -
44B PRO* 3.8 13.5 - - + -
47B VAL* 3.9 12.8 - - + -
128B LYS* 3.1 18.4 + - + +
129B GLY 3.7 2.5 - - - +
131B LYS* 1.3 76.9 - - - +
133B ALA* 1.3 69.4 + - - +
135B PHE* 2.7 5.3 + - + +
136B GLY* 2.6 26.0 + - - -
144B PHE* 4.0 15.2 - - + -
175B TYR* 3.5 51.4 - - + -
177B ILE* 4.1 15.4 - - + +
186B VAL* 5.4 0.2 - - + -
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Residues in contact with ALA 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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113B THR* 5.4 1.8 - - + +
115B LEU* 3.9 15.0 - - + -
129B GLY 2.9 13.9 + - - +
130B VAL* 3.2 14.8 - - - +
132B LEU* 1.3 77.5 - - - +
134B LYS* 1.3 60.0 + - - +
136B GLY* 4.0 0.5 - - - -
137B LYS* 3.4 23.4 + - - +
177B ILE* 4.4 4.6 - - - +
184B VAL* 3.5 29.0 - - + +
186B VAL* 3.6 19.4 - - + +
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Residues in contact with LYS 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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38B LEU 5.5 7.6 - - - +
115B LEU* 4.0 14.3 - - + +
117B LEU* 2.9 42.0 + - + +
130B VAL* 3.1 8.8 + - + +
131B LYS* 3.7 7.0 - - - +
132B LEU 3.0 0.6 - - - -
133B ALA* 1.3 78.0 - - - +
135B PHE* 1.3 65.0 + - - +
137B LYS* 4.3 2.9 - - - +
138B GLU* 3.2 50.9 + - - +
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Residues in contact with PHE 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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17B ILE* 4.7 12.8 - - + -
41B ASN* 3.1 43.1 - - - +
42B THR 3.7 24.2 - - - +
43B ILE* 3.7 31.4 - - + -
44B PRO* 5.1 1.6 - - + -
83B ILE* 6.1 2.9 - - + -
131B LYS* 3.0 13.7 + - + +
132B LEU* 2.7 16.2 + - + +
134B LYS* 1.3 71.2 - - - +
136B GLY* 1.3 68.9 + - - +
138B GLU* 3.9 3.1 + - - -
139B ASN* 3.1 38.6 + - - +
141B MET* 4.7 11.7 - - - -
144B PHE* 3.8 29.8 - + - -
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Residues in contact with GLY 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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132B LEU 2.6 18.7 + - - -
133B ALA 4.0 0.9 - - - -
135B PHE* 1.3 71.2 - - - +
137B LYS* 1.3 52.5 + - - +
138B GLU 2.5 1.1 + - - -
139B ASN 2.3 47.5 + - - +
141B MET* 3.5 20.9 - - - -
144B PHE* 4.2 12.8 - - - -
177B ILE* 4.9 3.4 - - - -
179B TRP* 4.6 0.2 - - - -
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Residues in contact with LYS 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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117B LEU* 3.0 50.3 - - + +
133B ALA 3.4 15.4 + - - +
134B LYS 4.3 2.2 - - - +
136B GLY* 1.3 69.6 - - - +
138B GLU* 1.3 66.5 + - + +
139B ASN 3.1 7.8 + - - +
140B LEU* 5.3 0.2 - - - -
179B TRP* 3.6 61.3 + - + -
181B GLY 4.5 11.3 + - - -
182B ASP* 5.2 1.6 - - - +
184B VAL* 4.1 4.5 - - + -
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Residues in contact with GLU 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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41B ASN* 5.0 9.3 + - - +
117B LEU* 4.8 6.9 - - + +
134B LYS* 3.2 52.8 + - + +
135B PHE* 4.4 3.4 - - - +
136B GLY 2.5 6.1 + - - -
137B LYS* 1.3 83.1 - - + +
139B ASN* 1.3 68.1 - - - +
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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