Contacts of the strand formed by residues 152 - 158 (chain G) in PDB entry 4U7B
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 ILE 152 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148G PHE* 3.8 21.1 - - + +
149G LEU* 3.1 26.6 + - + +
150G HIS 4.6 1.2 - - - +
151G ARG* 1.3 78.1 - - - +
153G VAL* 1.3 72.8 + - - +
154G THR* 4.1 12.3 - - - +
198G ASP* 3.1 24.1 - - - +
199G GLN 4.4 0.5 + - - -
245G ILE* 3.5 14.6 - - + +
247G LEU* 4.4 9.0 - - + -
271G LEU* 4.1 22.4 - - + -
282G PRO* 6.0 0.7 - - + -
326G ILE* 4.5 16.8 - - + -
329G LEU* 3.9 27.1 - - + -
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Residues in contact with VAL 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G ARG 4.2 2.2 - - - +
152G ILE* 1.3 75.6 - - - +
154G THR* 1.3 67.0 + - - +
196G TRP* 4.5 10.8 - - + -
197G TRP 3.6 15.3 - - - +
198G ASP* 4.4 5.8 - - + -
203G ILE* 4.5 8.7 - - + -
226G LEU* 5.0 3.1 - - + -
230G LEU* 4.4 20.6 - - + -
244G VAL* 3.4 38.4 - - + -
245G ILE 2.9 7.9 + - - +
246G PHE* 3.5 17.7 - - + -
247G LEU 3.2 20.4 + - - -
268G TRP* 5.8 0.7 - - + -
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Residues in contact with THR 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G ILE* 4.3 5.8 - - - -
153G VAL* 1.3 74.8 - - - +
155G GLY* 1.3 63.2 + - - +
196G TRP* 3.2 7.0 - - - +
197G TRP* 2.8 71.7 + - + +
247G LEU* 3.2 36.4 + - - +
281G ALA* 6.0 0.3 - - - +
282G PRO* 4.0 16.6 - - + +
283G SER* 3.6 9.4 + - - +
326G ILE* 4.1 7.2 - - + -
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Residues in contact with GLY 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G THR* 1.3 80.1 + - - +
156G ASP* 1.3 64.8 + - - +
195G VAL 3.1 14.8 - - - -
196G TRP* 3.6 18.4 - - - -
247G LEU 3.3 12.3 + - - +
248G HIS* 4.0 13.7 - - - +
249G ALA 4.6 1.2 + - - -
254G HIS* 5.9 0.5 - - - -
283G SER* 3.6 8.9 + - - -
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Residues in contact with ASP 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G GLY* 1.3 76.5 - - - +
157G GLU* 1.3 98.7 + - - +
193G LEU 3.9 0.5 - - - +
194G CYS* 3.7 2.5 - - - +
195G VAL* 3.2 31.1 + - - +
196G TRP* 4.9 4.3 - - - +
249G ALA* 4.3 21.5 + - - +
254G HIS* 5.9 2.2 - - - -
281G ALA* 5.0 4.9 - - - +
283G SER* 3.6 21.5 + - - -
284G ASP* 3.4 28.8 - - - +
288G PHE* 3.9 7.0 - - + -
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Residues in contact with GLU 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G ASP* 1.3 101.0 + - - +
158G LYS* 1.3 63.7 + - - +
192G MET* 3.4 36.0 - - + +
193G LEU 3.1 9.9 - - - +
194G CYS* 4.1 16.1 - - - +
196G TRP* 5.7 0.9 - - - -
214G VAL* 4.2 14.7 - - - +
219G TYR* 4.7 5.9 - - - -
222G GLN* 5.0 0.2 - - - +
249G ALA* 5.6 0.2 - - - +
251G ALA* 5.1 2.4 - - - +
253G SER* 5.6 0.6 + - - -
254G HIS* 3.1 37.6 + - - -
284G ASP* 5.1 1.0 - - - +
288G PHE* 3.8 5.5 - - - -
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Residues in contact with LYS 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157G GLU* 1.3 77.0 - - - +
159G TRP* 1.3 82.3 + - - +
160G ILE* 4.0 2.6 - - + +
192G MET* 4.5 3.1 - - - +
193G LEU* 2.9 36.2 + - + +
288G PHE* 3.3 57.3 + - + -
291G MET* 4.0 26.2 - - + -
292G GLY* 5.6 4.4 - - - +
295G LEU* 4.0 15.4 - - - +
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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