Contacts of the strand formed by residues 184 - 193 (chain E) in PDB entry 4YHP
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 TYR 184 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152E ASP 3.0 23.2 + - - -
153E TYR* 2.9 52.9 + + + +
154E PHE* 4.0 20.6 - + - -
155E PRO* 5.1 0.4 - - + -
156E GLU* 3.6 43.1 - - + +
176E ALA* 3.7 20.0 - - + -
177E VAL 3.4 8.5 - - - -
178E LEU* 3.5 31.9 - - + +
179E GLN* 3.4 0.6 + - - -
183E LEU* 1.3 73.7 - - - +
185E SER* 1.3 61.1 + - - +
110L THR* 3.2 18.8 - - + +
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Residues in contact with SER 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E LEU* 3.9 13.3 - - - +
150E VAL 3.3 12.7 + - - -
151E LYS* 3.8 15.6 - - - +
153E TYR* 4.1 1.6 - - - -
175E PRO 4.6 0.5 - - - +
176E ALA* 3.5 1.9 - - - -
177E VAL* 3.0 37.9 + - - +
179E GLN* 3.5 27.7 + - - -
184E TYR* 1.3 76.6 - - - +
186E LEU* 1.3 63.5 + - - +
179F THR* 6.1 0.7 - - - +
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Residues in contact with LEU 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E LEU* 3.7 7.0 - - - +
150E VAL* 2.7 60.3 + - + +
153E TYR* 3.3 25.4 - - + +
156E GLU* 5.1 1.3 - - - +
158E VAL* 4.4 16.6 - - + +
160E VAL* 4.3 7.9 - - + -
173E THR* 4.2 18.6 - - + -
174E PHE* 3.4 24.0 - - - +
175E PRO* 4.4 2.5 - - + +
176E ALA* 4.0 11.4 - - + +
185E SER* 1.3 75.8 + - - +
187E SER* 1.3 73.3 + - - +
163F SER* 6.5 0.2 - - - -
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Residues in contact with SER 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LEU* 3.6 23.0 - - - +
148E CYS 3.3 6.3 + - - -
149E LEU* 3.3 22.9 - - - +
173E THR 3.8 0.3 - - - -
174E PHE* 2.9 46.1 + - - +
186E LEU* 1.3 78.6 - - - +
188E SER* 1.3 60.7 + - - +
189E VAL* 4.5 4.0 - - - -
134F VAL* 4.3 8.7 - - - +
177F SER* 5.2 8.3 - - - -
179F THR* 5.3 1.7 + - - -
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Residues in contact with SER 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E GLY* 3.0 3.6 - - - -
148E CYS* 2.9 35.1 + - - +
150E VAL* 5.8 0.4 - - - -
160E VAL* 3.6 25.8 - - - +
162E TRP* 2.9 25.5 + - - -
171E VAL* 4.1 1.9 - - - +
172E HIS 3.3 5.0 + - - -
173E THR* 2.8 27.2 + - - +
186E LEU* 4.3 1.2 - - - +
187E SER* 1.3 74.3 - - - +
189E VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LEU* 4.0 21.5 - - + -
146E LEU 3.4 11.0 - - - +
147E GLY* 4.1 0.4 - - - -
162E TRP* 4.7 2.7 - - - -
171E VAL* 3.3 5.2 - - - +
172E HIS* 2.6 65.1 + - + +
174E PHE* 3.8 19.3 - - + -
187E SER* 4.5 4.0 - - - -
188E SER* 1.3 79.7 + - - +
190E VAL* 1.3 61.9 + - - +
191E THR* 6.3 0.4 - - + -
119F PHE* 4.8 4.9 - - + -
134F VAL* 5.8 2.0 - - + -
136F LEU* 3.9 32.5 - - + -
138F ASN* 5.0 0.7 - - - +
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Residues in contact with VAL 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E ALA 4.0 0.2 - - - +
145E ALA* 3.5 2.8 - - - +
146E LEU* 2.9 53.6 + - + +
162E TRP* 4.3 11.9 - - + -
167E LEU* 3.8 31.0 - - + -
169E SER 3.7 19.5 - - - +
170E GLY 3.4 5.6 - - - +
171E VAL* 3.8 12.3 - - + -
189E VAL* 1.3 78.1 - - - +
191E THR* 1.3 77.8 + - - +
192E VAL* 3.9 7.5 + - + -
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Residues in contact with THR 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E THR* 4.0 13.5 - - - +
144E ALA 3.2 9.9 - - - +
145E ALA* 4.2 13.0 - - + -
167E LEU* 5.9 0.2 - - - +
169E SER 4.5 5.4 - - - +
170E GLY* 3.4 19.0 + - - +
189E VAL* 6.3 0.2 - - + -
190E VAL* 1.3 81.0 - - - +
192E VAL* 1.3 63.3 + - - +
193E PRO* 4.9 0.2 - - - +
115F SER* 6.1 0.4 - - - -
117F PHE* 4.3 9.9 - - + -
136F LEU* 5.1 2.2 - - + -
138F ASN* 3.7 36.5 + - - +
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Residues in contact with VAL 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E THR* 3.6 5.3 - - - -
144E ALA* 2.7 42.7 + - + +
146E LEU* 4.0 22.4 - - + -
167E LEU* 4.7 4.3 - - + -
190E VAL* 3.9 20.0 - - + -
191E THR* 1.3 79.7 - - - +
193E PRO* 1.3 78.3 - - + +
196E SER* 3.9 4.5 - - - +
197E LEU* 4.2 10.3 - - + -
202E TYR* 3.5 35.0 - - + +
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Residues in contact with PRO 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ASN* 5.1 6.1 - - - +
171B ASP* 5.6 0.2 - - - +
142E GLY 3.8 11.0 - - - +
143E THR* 4.6 0.9 - - - -
192E VAL* 1.3 92.4 - - + +
194E SER* 1.3 63.4 + - - +
195E SER* 4.0 15.3 - - - +
196E SER* 2.4 37.8 + - - +
197E LEU 3.9 0.5 + - - -
202E TYR* 4.7 1.8 - - - +
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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
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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