Contacts of the helix formed by residues 125 - 142 (chain F) in PDB entry 3HYW
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 THR 125 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F ARG* 4.1 23.3 - - - +
45F PHE* 3.7 8.1 - - - -
109F LEU* 4.0 22.7 - - + -
123F ILE 3.9 0.5 - - - +
124F CYS* 1.3 82.3 - - + +
126F ALA* 1.3 59.4 + - - +
127F GLU* 3.6 16.9 + - - +
128F HIS* 2.9 33.6 + - + +
129F ALA* 2.8 30.5 + - - +
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Residues in contact with ALA 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F TYR* 3.6 12.5 + - - +
45F PHE* 3.5 24.0 - - + -
48F LEU* 3.6 14.5 - - + +
55F PHE* 3.6 35.9 - - + -
125F THR* 1.3 72.1 - - - +
127F GLU* 1.3 59.7 + - - +
129F ALA* 3.3 2.4 + - - +
130F LEU* 3.0 37.5 + - + +
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Residues in contact with GLU 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F ARG* 3.1 28.8 + - - +
38F TYR* 2.6 32.6 + - - -
125F THR* 3.6 10.2 - - - +
126F ALA* 1.3 78.9 + - - +
128F HIS* 1.3 62.3 + - + +
130F LEU* 3.4 10.2 + - + +
131F GLU* 3.3 27.1 + - - +
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Residues in contact with HIS 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F LEU* 4.0 13.1 - - + +
111F PHE* 3.9 18.8 - + - -
117F GLU* 5.4 8.0 + - + -
122F SER* 3.1 35.4 + - - +
124F CYS 5.5 0.2 - - - -
125F THR* 2.9 39.8 + - + +
127F GLU* 1.3 76.6 - - + +
129F ALA* 1.3 63.5 + - - +
131F GLU* 3.2 23.5 + - - +
132F THR* 3.0 25.3 + - - -
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Residues in contact with ALA 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F PHE* 3.6 25.8 - - + +
48F LEU* 3.9 12.8 - - + -
49F ALA* 3.3 18.5 - - + +
122F SER 3.7 7.8 + - - -
123F ILE* 4.3 8.3 - - - +
125F THR 2.8 20.8 + - - +
126F ALA* 3.6 5.2 - - - +
128F HIS* 1.3 72.2 - - - +
130F LEU* 1.3 62.7 + - - +
132F THR* 3.2 6.6 + - - -
133F GLN 3.1 17.5 + - - -
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Residues in contact with LEU 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 4.1 30.3 - - + +
55F PHE* 4.8 19.1 - - + +
126F ALA 3.0 26.6 + - - +
127F GLU* 3.8 8.5 - - + +
128F HIS 3.3 0.2 - - - -
129F ALA* 1.3 71.7 - - - +
131F GLU* 1.3 65.8 + - + +
133F GLN* 3.5 16.2 + - + +
134F LYS* 3.3 32.5 + - - +
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Residues in contact with GLU 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F THR* 5.1 2.5 - - + -
127F GLU* 3.3 12.5 + - - +
128F HIS* 3.2 33.9 + - - +
130F LEU* 1.3 77.2 - - + +
132F THR* 1.3 63.5 + - - +
134F LYS* 3.3 18.4 + - + +
135F LYS* 3.3 25.5 + - + +
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Residues in contact with THR 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ALA* 4.0 7.6 - - + -
121F THR* 3.3 34.7 - - - +
122F SER 2.7 27.5 + - - -
123F ILE* 4.2 3.8 - - + -
128F HIS 3.0 4.1 + - - -
129F ALA 3.2 9.6 + - - -
131F GLU* 1.3 75.3 - - - +
133F GLN* 1.3 59.8 + - - +
135F LYS* 3.1 4.3 + - - +
136F LEU* 2.9 27.7 + - + +
163F PHE* 3.8 22.9 - - + -
247F PHE* 3.8 13.9 - - + -
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Residues in contact with GLN 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LEU 4.2 4.0 - - - +
49F ALA 3.0 26.8 + - - +
50F MET 3.3 13.4 + - - +
51F GLY* 4.0 18.2 - - - -
129F ALA 3.1 10.6 + - - +
130F LEU* 3.8 13.0 - - + +
131F GLU 3.3 0.2 - - - -
132F THR* 1.3 75.6 - - - +
134F LYS* 1.3 63.4 + - + +
136F LEU* 3.2 10.0 + - - +
137F GLN* 2.9 48.2 + - - +
140F TYR* 4.8 4.0 + - - -
174F ARG* 5.9 0.4 - - - +
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Residues in contact with LYS 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LEU* 3.3 32.7 + - - +
131F GLU* 3.3 17.7 + - + +
132F THR 3.3 0.2 - - - -
133F GLN* 1.3 79.1 - - + +
135F LYS* 1.3 62.2 + - + +
137F GLN* 3.4 15.1 + - - +
138F GLU* 3.5 17.7 + - - +
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Residues in contact with LYS 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F GLU 5.0 3.0 + - - -
119F ASN* 3.1 31.9 + - - +
120F SER 4.3 4.7 + - - +
121F THR* 3.3 23.7 - - + +
131F GLU* 3.3 11.6 + - + +
132F THR 3.1 8.7 + - - +
134F LYS* 1.3 75.4 - - + +
136F LEU* 1.3 64.4 + - - +
138F GLU* 3.2 26.5 + - - +
139F LEU* 3.1 19.6 + - - +
246F LYS 5.7 4.2 + - - -
247F PHE* 3.9 21.9 - - + +
248F THR 5.8 2.0 + - - +
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Residues in contact with LEU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ALA 3.3 25.8 - - - +
50F MET* 3.7 18.8 - - - -
132F THR* 2.9 14.9 + - + +
133F GLN* 3.2 12.5 + - - +
135F LYS* 1.3 77.3 - - - +
137F GLN* 1.3 56.3 + - - +
139F LEU* 3.0 15.7 + - + +
140F TYR* 3.0 54.1 + - + +
163F PHE* 4.0 8.7 - - + -
167F LEU* 3.6 27.6 - - + -
247F PHE* 3.6 28.5 - - + -
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Residues in contact with GLN 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F GLN* 2.9 40.5 + - - +
134F LYS* 3.6 12.1 - - - +
135F LYS 3.3 0.4 - - - -
136F LEU* 1.3 76.2 - - - +
138F GLU* 1.3 60.4 + - + +
140F TYR* 3.5 17.3 + - - +
141F ALA* 3.3 21.7 + - - +
174F ARG* 3.9 21.6 + - - +
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Residues in contact with GLU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F LYS 3.5 14.2 + - - +
135F LYS* 3.2 29.3 + - - +
136F LEU 3.2 0.2 - - - -
137F GLN* 1.3 75.5 - - - +
139F LEU* 1.3 58.8 + - - +
141F ALA* 3.4 5.6 + - - +
142F ASN* 2.9 28.2 + - - +
246F LYS* 3.6 14.7 + - - +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F LYS 3.1 8.5 + - - +
136F LEU* 3.0 30.9 + - + +
138F GLU* 1.3 80.6 - - - +
140F TYR* 1.3 64.2 + - + +
142F ASN 3.1 0.3 - - - -
143F PRO* 3.0 30.8 - - + +
144F GLY 3.7 33.2 - - - +
146F VAL* 3.6 26.9 - - + -
167F LEU* 4.4 11.2 - - + -
171F LEU* 4.6 13.0 - - + -
176F ILE* 4.9 0.5 - - - +
180F VAL* 4.8 2.9 - - + -
246F LYS* 4.0 15.0 - - + +
247F PHE* 3.9 19.3 - - + -
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Residues in contact with TYR 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F MET* 3.6 17.8 + - - +
133F GLN* 4.8 4.5 + - - -
136F LEU* 3.0 44.4 + - + +
137F GLN* 3.5 24.0 + - - +
138F GLU 3.3 0.2 - - - -
139F LEU* 1.3 78.3 - - + +
141F ALA* 1.3 60.8 + - - +
143F PRO* 3.9 10.6 - - - +
167F LEU* 3.9 11.2 - - + +
170F GLU* 3.4 23.4 - - + +
171F LEU* 3.9 26.5 - - + -
174F ARG* 3.3 51.8 - - - +
176F ILE* 3.9 16.6 - - + +
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Residues in contact with ALA 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F GLN 3.3 14.7 + - - +
138F GLU* 3.8 6.3 - - - +
139F LEU 3.3 0.4 - - - -
140F TYR* 1.3 80.8 - - - +
142F ASN* 1.3 72.7 + - - +
143F PRO* 3.6 5.2 - - - +
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Residues in contact with ASN 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F GLU* 2.9 11.9 + - - +
139F LEU 3.1 4.6 - - - +
141F ALA* 1.3 91.1 - - - +
143F PRO* 1.3 67.5 - - - +
144F GLY 3.6 0.2 + - - -
246F LYS* 2.9 34.8 + - - +
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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