Contacts of the strand formed by residues 210 - 222 (chain A) in PDB entry 1SEK
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 THR 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A THR* 3.2 7.1 - - - +
194A MET 2.8 35.7 + - - +
196A ARG* 3.6 24.8 + - + +
197A ASP 5.4 0.9 + - - -
208A VAL* 2.9 22.7 + - - +
209A PRO* 1.3 74.3 + - - +
211A MET* 1.3 66.4 + - - +
212A ILE* 3.8 5.0 + - - +
280A TYR* 3.6 16.8 - - + +
281A LEU 3.5 30.3 - - - +
282A PRO* 3.8 5.5 - - + +
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Residues in contact with MET 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TRP* 4.9 0.4 - - - +
188A PHE* 3.6 27.6 - - + -
193A THR* 3.7 11.7 - - - +
210A THR* 1.3 73.6 - - - +
212A ILE* 1.3 60.1 + - - +
279A ILE 3.4 2.9 - - - +
280A TYR* 3.4 3.3 - - - -
281A LEU* 2.8 73.9 + - + +
282A PRO 4.0 7.9 - - - +
283A LYS* 3.6 23.3 - - + -
335A VAL* 4.3 5.8 - - + -
336A ASN* 3.3 40.2 - - - +
337A GLU* 3.4 18.8 - - + -
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PHE* 3.6 9.0 - - - +
189A ASN 4.5 6.6 + - - -
192A ARG* 3.6 57.8 + - + +
194A MET* 4.0 26.0 - - + -
196A ARG* 4.1 13.5 - - - +
210A THR 3.8 5.4 + - - +
211A MET* 1.3 81.5 - - - +
213A GLY* 1.3 58.5 - - - +
278A GLU* 3.2 23.6 - - - +
279A ILE 3.4 2.9 - - - +
280A TYR* 3.7 32.1 - - + +
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Residues in contact with GLY 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PHE* 3.7 11.7 - - - -
192A ARG* 5.1 9.0 - - - -
212A ILE* 1.3 78.3 - - - +
214A LYS* 1.3 63.4 + - - -
215A LYS* 3.7 14.0 + - - +
278A GLU* 3.6 8.5 - - - -
279A ILE* 2.8 32.1 + - - +
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Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ASP* 4.5 4.5 - - - +
192A ARG* 5.7 1.6 - - - +
213A GLY* 1.3 69.1 - - - -
215A LYS* 1.3 72.2 + - - +
276A GLU* 3.5 31.5 - - - +
277A VAL 3.3 7.6 - - - +
278A GLU* 3.7 20.4 + - - +
356A HIS* 4.6 8.6 + - - -
358A VAL* 3.2 42.4 - - + +
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TRP* 6.0 1.8 - - + -
186A ASP* 3.3 41.2 + - + +
187A LYS 3.1 19.3 + - - -
188A PHE* 3.6 44.2 - - + +
213A GLY* 3.9 17.4 - - - +
214A LYS* 1.3 81.9 + - - +
216A ASP* 1.3 65.4 + - - +
217A VAL* 3.4 19.5 + - + +
232A MET* 5.0 10.1 - - + -
276A GLU* 3.5 7.1 - - - -
277A VAL 2.9 30.9 + - - +
279A ILE* 5.1 5.2 - - + -
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Residues in contact with ASP 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 1.3 74.0 - - - +
217A VAL* 1.3 62.7 + - - +
231A GLU 5.0 0.2 - - - +
232A MET* 5.3 3.5 - - - +
233A SER* 5.5 2.4 + - - -
275A THR 3.4 8.6 - - - +
276A GLU* 3.1 28.6 + - - +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 3.8 13.2 - - + +
216A ASP* 1.3 80.6 - - - +
218A ARG* 1.3 71.6 + - - +
219A TYR* 4.4 7.0 - - + -
230A ILE* 4.1 11.9 - - + -
231A GLU 3.5 9.9 - - - +
232A MET* 3.7 27.4 - - + -
274A ASN* 3.6 6.1 - - - +
275A THR* 2.9 36.0 + - + +
277A VAL* 3.8 27.8 - - + -
279A ILE* 4.1 14.6 - - + -
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Residues in contact with ARG 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A VAL* 1.3 76.8 - - - +
219A TYR* 1.3 59.6 + - - +
229A MET 3.9 0.3 - - - +
230A ILE* 3.4 5.2 - - - +
231A GLU* 2.9 65.5 + - + +
269A GLU 5.3 2.6 + - - -
272A LEU* 3.9 36.7 + - + +
273A TYR* 3.4 7.4 - - - +
274A ASN* 3.6 36.0 - - - +
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Residues in contact with TYR 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A VAL* 4.0 6.0 - - + -
218A ARG* 1.3 75.8 - - - +
220A ALA* 1.3 88.6 + - - +
221A ASP* 4.0 8.1 - - + +
228A LYS* 3.1 44.0 + - + +
229A MET 3.4 16.2 - - - -
230A ILE* 3.9 15.5 - - + -
272A LEU* 4.0 1.8 - - - -
273A TYR* 2.9 60.1 + + + -
275A THR* 3.7 22.0 - - + -
277A VAL* 4.9 5.8 - - + -
361A VAL* 4.1 25.6 - - + -
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A TYR* 1.3 93.4 - - - +
221A ASP* 1.3 61.2 + - - +
222A VAL* 3.7 5.0 - - + +
228A LYS* 3.6 1.9 - - - -
229A MET* 2.8 34.8 + - + +
268A ALA 4.5 2.0 - - - +
271A ARG* 3.6 30.3 - - + +
272A LEU* 3.3 22.2 - - + -
273A TYR* 4.5 4.5 - - - -
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Residues in contact with ASP 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A TYR* 4.0 15.3 - - + +
220A ALA* 1.3 73.6 - - - +
222A VAL* 1.3 54.7 + - - +
223A PRO* 3.6 18.1 - - - +
227A ALA 4.0 7.4 - - - +
228A LYS* 4.0 18.8 + - - +
247A ASN* 4.8 9.0 + - - +
271A ARG* 2.6 43.3 + - - +
273A TYR* 5.5 0.8 - - - -
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Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ALA* 3.7 19.1 - - + +
221A ASP* 1.3 78.7 - - - +
223A PRO* 1.3 61.1 - - - +
224A GLU* 4.4 10.1 - - + +
225A LEU* 3.1 25.9 + - + +
226A ASP 2.9 22.5 + - - -
227A ALA* 2.9 22.7 + - + +
228A LYS 4.9 0.2 - - - -
229A MET* 4.1 18.4 - - + +
244A ILE* 6.1 0.7 - - + -
247A ASN* 6.0 0.4 - - - -
268A ALA* 3.8 33.0 - - + +
271A ARG* 4.0 10.8 - - - +
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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