Contacts of the strand formed by residues 237 - 248 (chain D) in PDB entry 1EVT
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 237 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D ALA* 4.4 3.1 - - - -
153D PRO* 3.4 15.0 - - - +
233D GLU* 3.1 4.2 - - - +
234D ASN* 2.8 32.4 + - - +
235D GLU 3.7 0.2 - - - -
236D TYR* 1.3 77.9 - - - +
238D SER* 1.3 60.9 + - - -
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Residues in contact with SER 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D PRO* 3.9 1.2 - - - +
231D ILE* 3.6 11.1 - - - +
232D VAL 3.1 10.3 + - - -
233D GLU* 3.3 29.4 + - - -
237D GLY* 1.3 73.7 - - - -
239D ILE* 1.3 66.6 + - - +
240D ASN* 5.1 5.1 + - - -
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Residues in contact with ILE 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ALA* 6.3 0.4 - - + -
153D PRO* 3.1 37.4 - - + +
154D TYR* 3.5 19.3 - - - +
155D TRP* 3.6 42.2 - - + +
180D SER* 4.5 1.1 - - - +
231D ILE* 3.7 1.6 - - - -
232D VAL* 2.8 42.3 + - + +
238D SER* 1.3 84.2 + - - +
240D ASN* 1.3 66.1 + - - +
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Residues in contact with ASN 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TRP* 3.2 17.7 + - - -
229D THR* 4.2 7.2 - - + +
230D CYS 3.3 14.8 - - - +
231D ILE* 4.0 13.7 - - + -
238D SER* 5.1 4.4 + - - -
239D ILE* 1.3 80.7 - - - +
241D HIS* 1.3 68.5 + - - +
242D THR* 5.2 1.9 + - - -
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Residues in contact with HIS 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TRP* 3.9 13.0 + - + -
161D MET* 3.3 42.5 + - + +
164D LYS* 5.2 5.6 - - + -
178D CYS* 4.3 1.3 - - - -
228D TYR 3.9 0.3 - - - +
229D THR* 3.1 4.2 - - - +
230D CYS* 3.0 41.9 + - - -
240D ASN* 1.3 81.2 + - - +
242D THR* 1.3 78.9 + - - +
243D TYR* 3.4 41.9 - + - -
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Residues in contact with THR 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D LYS* 4.7 8.5 - - - +
227D ASN* 3.6 31.4 - - + +
228D TYR 3.3 4.9 - - - +
229D THR* 2.5 27.7 + - - +
240D ASN* 5.2 2.3 + - - -
241D HIS* 1.3 92.4 + - - +
243D TYR* 1.3 67.3 + - - +
244D GLN 4.4 0.2 + - - -
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Residues in contact with TYR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D LYS 4.9 2.3 + - - -
161D MET* 3.5 22.8 - - - +
163D LYS 3.6 15.3 - - - -
164D LYS 3.5 11.2 - - - +
166D HIS* 3.6 26.0 - + - -
176D PHE* 3.8 39.5 - + + -
177D LYS* 2.4 34.2 + - - +
178D CYS* 3.9 11.0 - - - -
190D TRP* 4.5 4.3 - + - -
226D GLY 3.7 0.5 - - - +
227D ASN* 3.2 3.6 - - - -
228D TYR* 2.7 46.8 + - - +
241D HIS* 3.4 29.4 - + - -
242D THR* 1.3 77.5 - - - +
244D GLN* 1.3 61.0 + - - +
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Residues in contact with GLN 244 (chain D).
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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164D LYS* 3.1 8.7 + - + +
165D LEU* 3.3 28.0 - - + -
166D HIS* 2.9 28.1 + - - +
176D PHE* 4.4 0.2 - - - -
226D GLY 3.8 3.4 - - - -
227D ASN* 4.2 13.5 - - - +
242D THR 4.4 0.4 + - - -
243D TYR* 1.3 75.2 - - - +
245D LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D LEU* 4.7 0.4 - - - -
166D HIS* 3.4 8.1 - - + +
168D VAL* 5.2 0.9 - - + -
174D VAL* 3.3 43.7 - - + -
176D PHE* 3.3 19.7 - - + -
217D MET* 3.7 16.2 - - + -
220D VAL* 4.8 2.5 - - + -
224D ASP* 5.0 2.7 - - + +
225D LYS* 3.3 11.4 - - - +
226D GLY 2.9 37.4 + - - +
228D TYR* 3.9 10.5 - - + +
244D GLN* 1.3 73.5 - - - +
246D ASP* 1.3 69.5 + - - +
247D VAL* 3.4 29.6 - - + -
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Residues in contact with ASP 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ARG* 4.7 8.3 + - - +
135B LEU* 3.3 36.7 - - + +
136B PRO* 4.9 4.6 - - - +
165D LEU* 4.4 11.7 - - + -
166D HIS 2.8 7.8 + - - +
167D ALA* 3.2 11.4 - - + -
168D VAL 2.6 31.8 + - - -
225D LYS* 4.7 6.5 - - - +
244D GLN 4.2 0.4 - - - -
245D LEU* 1.3 79.1 - - - +
247D VAL* 1.3 67.7 + - - +
248D VAL* 4.1 3.2 - - - +
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Residues in contact with VAL 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D VAL* 3.0 4.5 - - + +
170D ALA* 3.4 35.4 - - + +
220D VAL* 3.7 21.5 - - + -
221D VAL* 4.0 13.0 - - - +
222D PRO* 3.9 32.0 - - + +
224D ASP* 4.9 0.2 - - + -
225D LYS* 4.8 8.4 - - + +
245D LEU* 3.4 26.9 - - + -
246D ASP* 1.3 80.8 + - - +
248D VAL* 1.3 70.7 + - - +
249D GLU 4.3 0.2 - - - -
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Residues in contact with VAL 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU* 4.6 8.3 - - + -
134B PRO* 3.6 14.1 - - + +
135B LEU* 3.2 35.9 - - + -
136B PRO* 5.1 6.3 - - + -
168D VAL 2.8 11.7 + - - +
169D PRO* 3.1 8.4 - - + +
170D ALA* 2.7 24.9 + - - -
246D ASP* 4.1 3.1 - - - +
247D VAL* 1.3 80.6 - - - +
249D GLU* 1.3 67.6 + - - +
250D ARG* 3.3 23.5 + - - +
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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