Contacts of the strand formed by residues 251 - 259 (chain E) in PDB entry 5HMG
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 LEU 251 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127E TRP* 4.0 15.0 - - + -
153E TRP* 4.3 0.3 - - - -
154E LEU* 3.7 33.1 + - + +
161E TYR* 3.8 10.2 + - - +
164E LEU* 4.3 6.7 - - + -
180E TRP* 4.9 7.0 - - + -
181E GLY 3.7 7.0 - - - +
202E VAL* 3.8 22.4 - - + -
245E ILE* 3.9 25.6 - - + -
247E SER* 3.7 23.3 - - - +
249E GLY 3.2 3.8 + - - -
250E ASN* 1.3 77.6 - - - +
252E ILE* 1.3 84.0 + - - +
253E ALA* 3.7 23.7 + - + +
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Residues in contact with ILE 252 (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 PHE* 4.1 16.2 - - + -
151E LEU* 3.8 41.5 - - + -
152E ASN 3.7 4.5 - - - +
153E TRP* 3.4 41.7 - - + +
180E TRP* 3.8 2.6 - - - +
181E GLY* 3.0 44.3 + - - +
182E ILE 4.1 12.8 - - - +
183E HIS* 4.1 9.9 - - + +
230E ILE* 4.3 13.0 - - + -
232E ILE* 5.8 0.2 - - + -
251E LEU* 1.3 79.0 - - - +
253E ALA* 1.3 59.7 + - - +
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Residues in contact with ALA 253 (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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127E TRP* 3.5 35.0 - - + -
151E LEU* 3.5 5.8 - - - +
152E ASN* 2.7 50.5 + - + +
154E LEU* 4.2 5.4 - - + -
251E LEU* 3.7 17.0 - - + -
252E ILE* 1.3 72.7 - - - +
254E PRO* 1.3 67.9 - - + +
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Residues in contact with PRO 254 (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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125E PHE* 3.6 19.6 - - + +
127E TRP* 4.6 1.8 + - + -
150E ARG 4.3 2.5 - - - +
152E ASN* 4.9 1.9 - - - +
178E TYR* 4.2 18.2 - - + -
179E ILE 3.5 25.1 - - - +
180E TRP* 3.9 16.4 - - + -
245E ILE* 3.5 31.2 - - + -
251E LEU* 5.0 2.2 - - + -
253E ALA* 1.3 94.4 - - + +
255E ARG* 1.3 61.9 + - - +
256E GLY 3.6 15.2 + - - +
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Residues in contact with ARG 255 (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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120E PHE* 3.6 13.4 - - + -
122E THR* 3.3 18.3 - - + +
123E GLU 2.9 20.8 + - - +
125E PHE* 4.3 5.8 - - - -
132E GLN* 4.4 2.8 - - - +
133E ASN* 2.7 44.1 + - - +
147E PHE* 5.9 2.2 - - - +
148E PHE 4.7 2.8 + - - -
149E SER* 3.3 24.3 + - - +
150E ARG 3.3 19.8 + - - +
151E LEU 2.6 33.5 + - - -
152E ASN* 3.3 27.5 + - + +
153E TRP 5.1 0.2 - - - +
254E PRO* 1.3 73.2 - - - +
256E GLY* 1.3 56.0 + - - +
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Residues in contact with GLY 256 (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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120E PHE* 3.3 11.2 - - - -
121E ILE 3.2 10.3 - - - -
123E GLU* 3.6 20.0 - - - -
125E PHE* 4.0 4.5 - - - -
178E TYR* 3.2 22.9 - - - -
179E ILE 5.1 1.0 + - - -
254E PRO* 3.3 9.2 + - - +
255E ARG* 1.3 77.4 + - - +
257E TYR* 1.3 59.8 + - - -
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Residues in contact with TYR 257 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119E GLU 3.8 0.2 - - - +
120E PHE* 3.2 8.7 - - - -
121E ILE* 2.9 75.9 + - + +
123E GLU* 3.5 26.7 - - + -
172E ASP* 3.8 7.8 + - - -
174E PHE* 3.4 39.6 - + - -
176E LYS* 3.5 40.2 - - + -
177E LEU 3.6 11.4 - - - +
178E TYR* 4.0 8.5 - - + -
256E GLY* 1.3 73.1 - - - +
258E PHE* 1.3 72.9 + - - +
259E LYS* 4.1 5.4 - - + -
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Residues in contact with PHE 258 (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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69E ALA 5.8 0.2 - - - -
70E LEU* 3.4 50.0 - - + -
71E LEU* 6.2 0.2 - - - -
117E THR 5.4 1.8 - - - +
118E LEU* 3.7 38.8 - - + -
119E GLU 3.5 2.7 - - - +
120E PHE* 3.9 28.5 - + + -
150E ARG* 3.9 14.8 - - + -
176E LYS* 3.8 0.7 - - - -
177E LEU* 2.9 61.6 + - + -
179E ILE* 3.8 19.5 - - + -
256E GLY 5.5 0.2 - - - -
257E TYR* 1.3 82.8 - - - +
259E LYS* 1.3 65.1 + - - +
260E MET* 3.7 0.4 + - + -
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Residues in contact with LYS 259 (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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115E SER* 3.5 1.6 + - - -
117E THR* 3.1 22.0 - - - +
119E GLU* 3.2 38.2 + - + +
121E ILE* 4.5 10.8 - - + -
174E PHE* 3.2 50.5 - - - +
175E ASP 4.5 2.7 - - - -
257E TYR* 4.0 19.0 + - + -
258E PHE* 1.3 76.5 - - - +
260E MET* 1.3 67.1 + - - +
261E ARG* 3.8 21.1 - - - +
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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