Contacts of the helix formed by residues 125 - 142 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ARG* 3.5 21.4 + - - +
45B PHE* 3.6 10.8 - - - -
109B LEU* 4.2 12.8 - - + -
123B ILE 3.9 0.9 - - - +
124B CYS* 1.3 80.5 - - + +
126B ALA* 1.3 58.9 + - - +
127B GLU* 3.6 15.2 + - - +
128B HIS* 3.0 40.1 + - + +
129B ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 5.7 0.2 - - - +
38B TYR* 3.7 12.5 + - + +
45B PHE* 3.4 23.1 - - + -
48B LEU* 3.8 14.8 - - + +
55B PHE* 3.7 36.1 - - + -
125B THR* 1.3 73.4 - - - +
127B GLU* 1.3 59.9 + - - +
129B ALA* 3.3 2.5 + - - +
130B LEU* 3.0 37.6 + - + +
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 3.2 28.7 + - - +
38B TYR* 2.6 37.3 + - - -
55B PHE* 5.2 1.0 - - - -
125B THR* 3.6 8.6 - - - +
126B ALA* 1.3 77.6 + - - +
128B HIS* 1.3 62.9 + - + +
130B LEU* 3.6 9.8 + - + +
131B GLU* 3.3 27.0 + - - +
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Residues in contact with HIS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 4.0 19.8 - - + +
111B PHE* 4.0 23.6 - + - -
117B GLU* 5.3 8.3 + - + -
122B SER* 3.1 33.4 + - - +
123B ILE 4.5 0.2 - - - +
124B CYS 4.5 0.2 - - - +
125B THR* 3.0 32.2 + - + +
127B GLU* 1.3 75.1 - - + +
129B ALA* 1.3 65.9 + - - +
131B GLU* 3.2 11.5 + - - +
132B THR* 2.9 24.4 + - - -
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Residues in contact with ALA 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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45B PHE* 3.4 27.6 - - + +
48B LEU* 4.1 10.8 - - + -
49B ALA* 3.3 21.2 - - + +
122B SER 3.6 7.5 + - - -
123B ILE* 4.2 6.5 - - - +
125B THR 2.9 17.4 + - - +
126B ALA* 3.6 5.6 - - - +
128B HIS* 1.3 76.2 - - - +
130B LEU* 1.3 56.7 + - - +
132B THR* 3.1 5.2 + - - -
133B GLN 2.9 24.3 + - - -
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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
----------------------------------------------------------
48B LEU* 3.9 30.3 - - + -
55B PHE* 4.7 20.4 - - + +
126B ALA 3.0 24.1 + - - +
127B GLU* 3.9 9.4 - - + +
129B ALA* 1.3 76.6 - - - +
131B GLU* 1.3 67.5 + - - +
133B GLN* 3.4 21.5 + - - +
134B LYS* 3.4 26.9 + - + +
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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
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121B THR* 5.0 2.9 - - + +
127B GLU 3.3 14.9 + - - +
128B HIS* 3.2 14.2 + - - +
130B LEU* 1.3 78.6 - - - +
132B THR* 1.3 65.7 + - - +
134B LYS* 3.3 35.2 + - - +
135B LYS* 3.2 20.8 + - - +
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 4.0 13.0 - - + -
121B THR* 3.3 36.3 - - - +
122B SER 2.6 28.3 + - - -
123B ILE* 4.0 4.5 - - + -
128B HIS 2.9 4.2 + - - -
129B ALA 3.1 8.7 + - - -
131B GLU* 1.3 76.5 - - - +
133B GLN* 1.3 62.7 + - - +
135B LYS* 3.1 3.6 + - - +
136B LEU* 2.9 23.3 + - + +
163B PHE* 3.9 27.1 - - + -
247B PHE* 4.0 4.7 - - + -
249B MET* 4.4 0.2 - - + -
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 2.7 22.9 - - - +
49B ALA 3.1 21.9 + - - +
50B MET 4.6 0.7 - - - -
51B GLY* 3.5 23.8 + - - +
53B ARG 4.7 2.2 + - - +
129B ALA 2.9 11.1 + - - +
130B LEU* 3.4 27.6 - - - +
131B GLU 3.3 0.2 - - - -
132B THR* 1.3 74.8 - - - +
134B LYS* 1.3 64.0 + - + +
136B LEU* 3.3 13.2 + - - +
137B GLN* 3.4 21.9 + - + +
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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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130B LEU* 3.4 16.4 - - + +
131B GLU* 3.3 35.2 + - - +
132B THR 3.3 0.2 - - - -
133B GLN* 1.3 77.8 - - + +
135B LYS* 1.3 60.9 + - - +
137B GLN* 3.3 22.8 + - - +
138B GLU* 3.8 4.5 + - - +
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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
----------------------------------------------------------
119B ASN 3.4 24.3 + - - +
120B SER* 4.4 0.9 - - - +
121B THR* 3.3 23.2 - - + +
131B GLU 3.2 11.2 + - - +
132B THR 3.1 8.5 + - - +
134B LYS* 1.3 75.3 - - - +
136B LEU* 1.3 62.7 + - - +
138B GLU* 3.3 23.1 + - + +
139B LEU 3.5 4.3 + - - -
246B LYS 4.5 10.6 + - - -
247B PHE* 3.9 20.7 - - + +
248B THR 3.7 32.7 + - - +
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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
----------------------------------------------------------
49B ALA 3.4 24.9 - - - +
50B MET* 3.9 15.7 - - - -
132B THR* 2.9 12.7 + - + +
133B GLN 3.4 8.3 - - - +
134B LYS 3.2 0.2 - - - -
135B LYS* 1.3 76.2 - - - +
137B GLN* 1.3 64.1 + - - +
139B LEU* 3.1 24.9 + - + +
140B TYR* 3.1 36.6 + - + +
163B PHE* 3.7 18.8 - - + -
167B LEU* 3.8 25.4 - - + -
247B PHE* 3.6 29.8 - - + -
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Residues in contact with GLN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 3.4 19.9 + - + +
134B LYS* 3.3 13.0 + - - +
135B LYS 3.3 0.6 - - - -
136B LEU* 1.3 76.4 - - - +
138B GLU* 1.3 61.3 + - - +
140B TYR* 3.6 28.9 + - - +
141B ALA* 3.4 21.0 + - - +
174B ARG* 3.9 14.7 + - - +
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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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134B LYS 3.8 4.4 + - - +
135B LYS* 3.3 17.6 + - + +
136B LEU 3.2 0.6 - - - -
137B GLN* 1.3 77.6 - - - +
139B LEU* 1.3 58.6 + - - +
141B ALA* 3.2 6.8 + - - +
142B ASN* 3.0 46.2 + - - +
246B LYS* 3.3 26.7 + - - +
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Residues in contact with LEU 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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135B LYS 3.5 6.4 + - - +
136B LEU* 3.1 33.5 + - + +
138B GLU* 1.3 79.1 - - - +
140B TYR* 1.3 65.5 + - + +
142B ASN 4.1 4.9 - - - +
143B PRO* 3.1 30.5 - - + +
144B GLY* 3.5 35.2 - - - +
146B VAL* 3.6 25.1 - - + -
167B LEU* 4.3 13.2 - - + -
171B LEU* 4.6 12.6 - - + -
176B ILE* 5.0 0.5 - - - +
180B VAL* 4.5 3.4 - - + -
246B LYS* 4.3 7.0 - - + +
247B PHE* 4.0 19.5 - - + -
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Residues in contact with TYR 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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50B MET* 3.6 19.1 + - - +
136B LEU* 3.1 40.2 + - + +
137B GLN* 3.7 31.2 - - - +
138B GLU 3.3 0.4 - - - -
139B LEU* 1.3 76.7 - - + +
141B ALA* 1.3 61.3 + - - +
143B PRO* 4.0 6.2 - - - +
167B LEU* 3.9 10.3 - - + +
170B GLU* 3.4 22.8 - - + +
171B LEU* 3.9 27.6 - - + -
174B ARG* 3.5 51.4 - - - +
176B ILE* 3.9 19.0 - - + +
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Residues in contact with ALA 141 (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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137B GLN 3.4 10.4 + - - +
138B GLU* 3.2 12.3 + - - +
139B LEU 3.2 0.4 - - - -
140B TYR* 1.3 80.8 - - - +
142B ASN* 1.3 71.7 + - - +
143B PRO* 3.4 8.0 - - - +
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Residues in contact with ASN 142 (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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138B GLU* 3.0 22.6 + - - +
139B LEU* 3.2 5.5 - - - +
141B ALA* 1.3 86.1 - - - +
143B PRO* 1.3 71.4 - - - +
144B GLY 3.6 0.2 + - - -
246B LYS* 2.8 44.2 + - - +
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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