Contacts of the strand formed by residues 214 - 224 (chain B) in PDB entry 4EOH
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 VAL 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B ARG* 3.6 32.1 - - - +
207B ARG 3.4 11.7 - - - +
208B ARG* 3.6 42.2 - - + +
212B GLY 3.8 0.2 + - - -
213B SER* 1.3 70.8 - - - +
215B VAL* 1.3 68.2 + - - +
404B MPD 4.5 16.4 - - + +
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B GLN 3.9 0.3 - - - +
206B ARG* 3.3 5.5 - - - +
207B ARG* 2.8 60.8 + - + +
209B ASN* 4.3 20.4 - - + +
213B SER* 4.1 15.3 - - - +
214B VAL* 1.3 79.6 - - - +
216B MET* 1.3 64.2 + - - +
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Residues in contact with MET 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ASP* 3.5 22.0 - - - +
176B HIS* 3.6 9.0 - - + -
204B SER* 3.4 19.3 - - - +
205B GLN 3.2 9.4 - - - +
206B ARG* 3.3 40.8 - - + +
215B VAL* 1.3 81.1 - - - +
217B GLU* 1.3 65.3 + - - +
218B ARG* 3.7 27.2 + - + +
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Residues in contact with GLU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B SER* 3.3 3.3 - - - -
205B GLN 2.8 31.8 + - - +
207B ARG* 2.7 52.0 + - - +
216B MET* 1.3 73.6 - - - +
218B ARG* 1.3 64.6 + - - +
219B ILE* 4.1 8.6 - - + +
250B ASN 3.8 1.6 - - - +
251B ASN* 3.9 4.0 - - - +
252B LEU* 3.1 25.4 + - + +
253B LYS* 3.2 30.8 + - - +
311B VAL* 6.2 2.7 - - + -
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Residues in contact with ARG 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LEU* 3.7 46.3 + - + +
172B MET* 6.2 0.6 - - - +
173B ASP* 3.1 36.6 + - - -
203B GLY 3.2 6.1 - - - +
204B SER* 4.0 17.2 + - - +
216B MET* 3.7 20.3 + - + +
217B GLU* 1.3 79.3 - - - +
219B ILE* 1.3 68.6 + - - +
311B VAL* 3.9 3.5 - - - +
312B LEU* 2.9 57.1 + - + +
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LEU* 5.8 0.5 - - - +
201B VAL* 4.6 3.8 - - + +
202B LEU* 3.5 5.5 - - - +
203B GLY* 2.9 40.8 + - - +
217B GLU* 4.1 12.8 - - + +
218B ARG* 1.3 80.9 - - - +
220B ARG* 1.3 69.6 + - - +
221B MET* 4.2 17.7 - - + -
252B LEU* 3.9 21.8 - - + -
253B LYS* 4.0 32.3 - - + +
256B CYS* 4.2 20.4 - - + -
309B ALA* 4.1 6.7 - - + -
310B THR 3.4 11.4 - - - +
311B VAL* 5.0 4.9 - - + -
312B LEU* 3.9 8.9 - - - +
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Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLN* 2.5 44.8 + - - +
190B LEU* 5.6 2.4 - - - +
191B PRO 3.2 18.8 + - - -
193B PRO* 3.5 13.2 - - - +
200B ILE* 3.0 39.1 - - + +
201B VAL 3.2 6.7 - - - +
202B LEU* 3.7 11.4 - - + -
219B ILE* 1.3 77.7 - - - +
221B MET* 1.3 67.1 + - - +
222B ASP* 3.0 24.9 + - - +
309B ALA* 3.2 4.2 - - - -
310B THR* 2.7 51.2 + - - +
312B LEU* 3.7 16.6 - - + -
405B MPD 3.9 16.8 - - - +
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Residues in contact with MET 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B ILE* 3.4 5.5 - - - +
201B VAL* 2.8 40.5 + - + +
219B ILE* 4.2 7.0 - - + -
220B ARG* 1.3 80.1 - - - +
222B ASP* 1.3 67.0 + - - +
223B ILE* 3.3 15.7 - - + +
256B CYS* 3.8 26.7 - - - +
257B GLU* 4.0 11.7 - - + -
260B VAL* 3.7 31.4 - - + -
307B VAL* 3.3 41.1 - - + -
308B GLN 5.1 2.5 - - - -
309B ALA* 3.5 18.8 - - + +
310B THR* 6.2 0.7 - - - -
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Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B SER* 2.6 27.6 + - - +
193B PRO* 3.4 8.2 - - - +
194B GLN* 3.6 22.6 - - - +
198B TYR* 3.7 10.2 - - + -
199B LEU 3.4 5.8 - - - +
200B ILE* 2.8 16.0 - - - +
220B ARG* 3.0 30.7 + - - +
221B MET* 1.3 72.5 - - - +
223B ILE* 1.3 61.3 + - - +
307B VAL* 4.7 8.2 - - - +
308B GLN 5.7 0.4 + - - -
310B THR* 5.1 5.2 + - - +
411B MPD 4.0 10.4 - - - +
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Residues in contact with ILE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B TYR* 3.2 3.5 - - - -
199B LEU* 2.7 53.8 + - + +
201B VAL* 3.7 21.1 - - + -
221B MET* 3.3 38.8 - - + +
222B ASP* 1.3 75.0 - - - +
224B ARG* 1.3 66.6 + - - +
225B LYS 3.4 0.2 + - - -
260B VAL* 3.9 23.1 - - + -
307B VAL* 5.1 4.0 - - + -
408B MPD 4.3 9.2 - - + -
410B MPD 3.2 36.1 - - + -
411B MPD 3.2 9.4 - - - +
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Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ASN* 3.0 53.5 + - - +
198B TYR* 3.2 42.0 + - + -
199B LEU* 5.1 0.5 - - - +
223B ILE* 1.3 73.5 - - - +
225B LYS* 1.3 75.6 + - - +
226B VAL* 4.2 0.2 - - - +
410B MPD 2.7 39.4 - - + +
411B MPD 2.9 34.2 + - + +
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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