Contacts of the strand formed by residues 238 - 249 (chain G) in PDB entry 1EV2
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 GLY 238 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153G ALA* 4.1 2.0 - - - -
154G PRO* 3.4 14.7 - - - +
234G GLU* 3.2 5.0 - - - +
235G ASN* 3.1 33.4 + - - +
236G GLU 3.5 1.2 + - - -
237G TYR* 1.3 80.2 - - - +
239G SER* 1.3 59.7 + - - -
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Residues in contact with SER 239 (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 PRO* 4.4 0.2 - - - +
232G VAL* 3.8 14.0 - - - +
233G VAL 3.4 5.8 - - - -
234G GLU* 2.9 27.6 + - - +
238G GLY* 1.3 74.5 - - - -
240G ILE* 1.3 69.9 + - - +
241G ASN* 5.5 0.6 - - - +
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Residues in contact with ILE 240 (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 PRO* 3.6 38.6 - - + +
155G TYR* 3.8 11.2 - - - +
156G TRP* 3.6 42.0 - - + +
232G VAL* 3.6 1.6 - - - +
233G VAL* 3.0 36.7 + - + +
239G SER* 1.3 83.3 + - - +
241G ASN* 1.3 64.4 + - - +
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Residues in contact with ASN 241 (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 TRP* 3.9 10.3 + - - -
230G THR* 4.0 16.2 - - + +
231G CYS 3.1 14.8 - - - +
232G VAL* 4.4 10.0 - - + +
239G SER 5.5 0.3 - - - +
240G ILE* 1.3 78.5 - - - +
242G HIS* 1.3 65.6 + - - +
243G THR* 4.8 4.2 + - - -
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Residues in contact with HIS 242 (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 TRP* 4.1 4.9 + - + +
162G MET* 3.3 58.0 + - + +
165G ARG* 5.3 5.1 - - + -
179G CYS* 4.4 0.2 - - - -
229G TYR 4.0 0.7 - - - +
230G THR* 3.3 4.0 - - - +
231G CYS* 3.1 37.1 + - - -
241G ASN* 1.3 78.9 + - - +
243G THR* 1.3 74.0 + - - +
244G TYR* 3.4 42.4 + + - -
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Residues in contact with THR 243 (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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165G ARG* 4.4 11.3 - - - +
228G ASN* 4.1 11.9 - - + +
229G TYR 3.6 2.9 - - - +
230G THR* 2.7 28.6 + - - +
241G ASN* 4.8 5.6 + - - +
242G HIS* 1.3 91.1 + - - +
244G TYR* 1.3 76.3 + - - +
245G HIS* 4.0 24.2 + - + -
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Residues in contact with TYR 244 (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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161G LYS 3.6 6.3 + - - -
162G MET* 3.5 23.5 - - - +
164G LYS 3.3 27.1 - - - -
165G ARG* 3.5 6.7 - - - -
167G HIS* 4.1 9.2 - + - -
177G PHE* 3.4 55.0 - + + -
178G ARG 2.7 32.2 + - - -
179G CYS* 4.0 6.7 - - - -
191G TRP* 4.4 4.5 - + - -
228G ASN* 3.3 4.7 - - - -
229G TYR* 2.8 40.3 + - - +
242G HIS* 3.4 30.5 - + - -
243G THR* 1.3 76.6 - - - +
245G HIS* 1.3 63.8 + - - +
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Residues in contact with HIS 245 (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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165G ARG* 2.9 24.1 + - + +
166G LEU* 3.5 17.5 - - + +
167G HIS* 2.8 29.3 + - - +
177G PHE* 5.0 0.2 - - - -
227G GLY 3.5 4.3 - - - +
228G ASN* 2.3 38.9 + - - +
243G THR* 4.0 21.7 + - + +
244G TYR* 1.3 75.4 + - - +
246G LEU* 1.3 60.2 + - - +
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Residues in contact with LEU 246 (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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166G LEU* 4.9 0.4 - - - -
167G HIS* 3.2 24.2 - - + +
169G VAL* 4.3 6.1 - - + -
175G VAL* 4.1 28.0 - - + -
177G PHE* 4.0 7.6 - - + -
218G MET* 4.1 16.6 - - + -
221G VAL* 4.7 2.5 - - + -
225G ASP* 3.7 31.6 - - + +
226G LYS* 3.2 6.6 - - - +
227G GLY 2.9 28.0 + - - +
229G TYR* 3.9 22.9 - - + -
244G TYR 4.2 0.4 - - - -
245G HIS* 1.3 75.3 - - - +
247G ASP* 1.3 75.0 + - - +
248G VAL* 4.4 7.4 - - + -
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Residues in contact with ASP 247 (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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142C MET* 3.7 31.7 - - + +
166G LEU* 4.5 9.8 - - + +
167G HIS 3.0 7.0 + - - +
168G ALA* 3.3 7.1 - - + -
169G VAL 2.9 26.2 + - - +
226G LYS* 4.6 9.7 - - - +
245G HIS 4.2 0.2 + - - -
246G LEU* 1.3 79.8 - - - +
248G VAL* 1.3 74.4 + - - +
249G VAL* 5.2 1.1 - - - +
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Residues in contact with VAL 248 (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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169G VAL 3.3 4.5 - - - +
171G ALA* 3.5 35.7 - - + +
221G VAL* 3.7 24.2 - - + -
222G VAL 3.4 33.9 - - - +
223G PRO* 3.9 16.0 - - + +
225G ASP* 4.5 3.1 - - + -
226G LYS* 4.8 6.7 - - - +
246G LEU* 4.4 14.1 - - + -
247G ASP* 1.3 84.5 + - - +
249G VAL* 1.3 69.8 + - - +
250G GLU 4.4 0.5 + - - -
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Residues in contact with VAL 249 (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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140C LEU* 3.8 29.4 - - + -
141C PRO* 4.0 14.8 - - + +
142C MET* 4.1 27.8 - - + -
169G VAL 3.0 6.9 + - - -
170G PRO* 3.2 7.1 - - - +
171G ALA 2.8 23.2 + - - -
247G ASP* 5.1 1.6 - - - +
248G VAL* 1.3 81.1 - - - +
250G GLU* 1.3 73.2 + - - +
251G ARG* 3.6 14.8 + - - +
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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