Contacts of the helix formed by residues 137 - 151 (chain B) in PDB entry 4YP9
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 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B LEU* 3.8 7.3 - - - +
136B ASP* 1.3 82.9 + - - +
138B THR* 1.3 75.3 + - - +
139B ARG* 3.5 55.3 + - + +
140B HIS* 3.3 29.8 + - - +
141B ARG* 3.5 9.3 + - - +
208B GLU 4.5 11.6 + - - +
209B GLY* 4.8 3.4 - - - -
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Residues in contact with THR 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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137B THR* 1.3 77.2 - - - +
139B ARG* 1.3 66.5 + - - +
140B HIS 3.1 0.4 - - - -
141B ARG* 3.1 30.0 + - + +
142B LYS* 3.5 16.7 + - - +
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Residues in contact with ARG 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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113B ILE* 3.4 51.1 - - + +
116B GLN* 3.3 33.1 + - - +
117B SER* 5.7 2.0 + - - +
120B LEU* 5.6 1.8 - - - +
137B THR* 3.1 33.7 + - + +
138B THR* 1.3 81.0 - - - +
140B HIS* 1.3 76.0 + - + +
142B LYS* 3.7 13.5 + - - +
143B PHE* 3.7 10.9 + - - +
208B GLU 5.9 0.2 + - - -
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Residues in contact with HIS 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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116B GLN* 5.3 3.0 + - - -
120B LEU* 5.0 7.9 - - + -
133B PHE* 3.8 27.8 - + + -
134B THR* 3.6 22.0 + - - -
135B LEU* 3.8 11.1 - - + -
136B ASP* 3.3 24.4 + - + -
137B THR* 3.3 30.6 + - - +
138B THR 3.1 0.4 - - - -
139B ARG* 1.3 94.9 + - + +
141B ARG* 1.3 58.6 + - - +
143B PHE* 3.3 4.3 + - - +
144B VAL* 2.9 35.0 + - - +
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Residues in contact with ARG 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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28B TYR* 3.2 31.7 + - - -
135B LEU* 3.8 20.2 - - + -
137B THR 3.5 12.3 + - - +
138B THR* 3.1 22.9 + - + +
140B HIS* 1.3 78.1 - - - +
142B LYS* 1.3 60.2 + - + +
144B VAL* 3.2 3.9 + - - +
145B GLU* 2.8 46.1 + - - +
164B VAL* 3.6 26.1 - - - +
166B GLU* 3.9 18.8 + - - +
167B TRP* 3.7 22.4 - - - -
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Residues in contact with LYS 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 THR* 3.6 16.2 - - - +
139B ARG* 4.0 9.2 - - - +
140B HIS 3.3 0.4 - - - -
141B ARG* 1.3 77.6 - - + +
143B PHE* 1.3 58.6 + - - +
145B GLU* 3.3 13.7 + - - +
146B HIS* 2.8 29.2 + - - +
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Residues in contact with PHE 143 (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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72B VAL* 6.0 1.6 - - + -
117B SER* 5.0 1.3 - - - -
120B LEU* 3.6 56.3 - - + -
121B MET* 4.1 15.9 - - + -
124B LEU* 3.9 22.9 - - + -
131B LEU* 4.7 13.7 - - + -
133B PHE* 4.0 36.6 - + + -
139B ARG 3.7 9.2 + - - +
140B HIS 3.3 7.1 + - - +
141B ARG 3.2 0.2 - - - -
142B LYS* 1.3 77.1 - - - +
144B VAL* 1.3 64.5 + - + +
146B HIS* 3.1 7.6 + - + +
147B VAL* 2.9 48.8 + - + +
155B LEU* 5.9 0.9 - - + -
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Residues in contact with VAL 144 (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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133B PHE* 3.7 28.0 - - + -
134B THR 4.6 1.6 - - - +
135B LEU* 4.7 7.2 - - + -
140B HIS 2.9 22.3 + - - +
141B ARG 3.6 4.3 - - - +
143B PHE* 1.3 78.9 - - + +
145B GLU* 1.3 57.1 + - - +
147B VAL* 3.1 8.2 + - - +
148B LEU* 2.8 33.4 + - + +
155B LEU* 3.6 22.0 - - + -
157B LEU* 4.0 13.0 - - + -
167B TRP* 3.2 33.7 - - + -
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Residues in contact with GLU 145 (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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141B ARG* 2.8 33.4 + - - +
142B LYS* 3.5 15.4 + - - +
144B VAL* 1.3 73.4 - - - +
146B HIS* 1.3 57.5 + - - +
148B LEU* 3.7 5.8 - - - -
149B ASP* 2.8 46.9 + - - +
166B GLU* 4.0 17.8 - - - +
167B TRP* 3.2 36.9 + - + +
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Residues in contact with HIS 146 (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 MET* 3.7 36.1 - - + +
124B LEU* 3.9 10.9 - - + +
142B LYS 2.8 14.4 + - - +
143B PHE* 3.1 12.8 + - + +
145B GLU* 1.3 73.2 - - - +
147B VAL* 1.3 67.5 + - - +
149B ASP* 4.6 3.6 - - - -
150B SER* 2.9 52.5 + - - -
151B THR* 4.8 3.4 - - + -
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Residues in contact with VAL 147 (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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124B LEU* 3.9 20.0 - - + -
131B LEU* 5.0 4.5 - - + -
143B PHE* 2.9 54.0 + - + +
144B VAL* 3.4 9.2 - - - +
146B HIS* 1.3 73.8 + - - +
148B LEU* 1.3 62.6 + - - +
151B THR* 2.6 44.0 + - - +
153B THR* 4.4 11.8 - - + +
155B LEU* 4.2 31.9 - - + -
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Residues in contact with LEU 148 (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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144B VAL* 2.8 39.5 + - + +
145B GLU* 3.8 4.7 - - - +
147B VAL* 1.3 75.4 - - + +
149B ASP* 1.3 67.6 + - - +
151B THR 4.2 6.6 - - - +
153B THR 5.9 1.3 - - - +
155B LEU* 4.0 20.0 - - + -
167B TRP* 3.9 31.0 - - + +
170B HIS* 3.1 54.4 + - + +
172B PRO* 3.9 31.6 - - + -
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Residues in contact with ASP 149 (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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145B GLU* 2.8 37.6 + - - +
146B HIS* 4.0 3.4 - - - +
148B LEU* 1.3 81.0 - - - +
150B SER* 1.3 61.5 + - - +
151B THR 3.8 0.6 + - - -
167B TRP* 6.2 0.2 - - - -
170B HIS* 5.1 3.5 - - - +
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Residues in contact with SER 150 (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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146B HIS* 2.9 50.4 + - - -
149B ASP* 1.3 81.2 - - - +
151B THR* 1.3 63.1 + - - +
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Residues in contact with THR 151 (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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124B LEU* 4.6 21.0 - - + +
127B LYS* 6.4 2.0 - - - -
146B HIS* 4.8 2.2 - - + +
147B VAL* 2.6 36.5 + - - +
148B LEU 4.2 6.2 - - - +
149B ASP 3.8 1.2 - - - -
150B SER* 1.3 95.1 - - - +
152B ASN* 1.3 67.0 + - - +
153B THR* 3.5 23.1 + - - +
170B HIS* 5.1 3.6 + - - -
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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