Contacts of the strand formed by residues 221 - 238 (chain A) in PDB entry 1C5G
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 SER 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A ARG* 3.1 32.1 + - - +
210A ARG 3.2 6.5 + - - -
211A LEU* 3.9 13.0 - - - +
220A VAL* 1.3 72.9 - - - +
222A VAL* 1.3 62.1 + - - +
223A PRO* 3.3 11.4 - - - +
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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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209A ARG* 4.3 0.4 - - - -
210A ARG* 2.8 40.0 + - + +
213A HIS* 3.7 30.3 - - + +
220A VAL* 3.7 13.0 + - + +
221A SER* 1.3 70.5 - - - +
223A PRO* 1.3 82.9 - - + +
224A MET* 4.3 1.3 - - - -
299A PRO* 4.1 11.0 - - + -
300A LYS 5.4 1.8 - - - +
400A MET* 4.2 20.6 - - + -
402A PRO* 3.6 27.6 - - + -
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Residues in contact with PRO 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A THR* 5.1 5.6 - - + -
208A HIS 3.6 5.4 - - - +
209A ARG* 4.1 18.4 - - - +
221A SER 3.3 10.5 - - - +
222A VAL* 1.3 97.4 - - + +
224A MET* 1.3 61.4 + - - +
300A LYS* 3.4 54.1 + - + +
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Residues in contact with MET 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A THR* 3.0 8.9 - - - +
208A HIS* 2.5 66.8 + - + +
210A ARG* 3.7 36.8 - - + +
222A VAL* 4.1 11.0 - - - +
223A PRO* 1.3 83.3 - - - +
225A MET* 1.3 69.8 + - - +
297A VAL* 4.8 13.5 - - + -
298A LEU 4.0 4.5 - - - +
299A PRO* 4.1 21.3 - - + -
402A PRO* 3.8 29.8 - - + +
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Residues in contact with MET 225 (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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202A PHE* 3.9 26.0 - - + -
206A SER 4.2 3.4 - - - -
207A THR* 4.2 5.4 - - - +
224A MET* 1.3 78.2 - - - +
226A ALA* 1.3 64.9 + - - +
297A VAL* 3.3 5.8 - - - +
298A LEU* 2.9 67.9 + - + +
299A PRO 4.2 7.6 - - - +
300A LYS* 4.0 13.2 - - + -
351A VAL* 4.3 7.0 - - + -
352A ASN* 3.4 12.1 - - - +
353A GLU* 3.4 52.7 - - - +
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Residues in contact with ALA 226 (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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202A PHE* 3.8 3.8 - - - +
203A PRO* 3.2 18.0 + - - +
206A SER* 3.2 33.6 - - - +
208A HIS* 4.7 4.5 - - + -
225A MET* 1.3 78.1 - - - +
227A GLN* 1.3 66.3 + - - +
295A LEU* 4.6 9.2 - - + -
296A LEU 3.2 7.9 - - - +
297A VAL* 3.6 20.9 - - + -
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Residues in contact with GLN 227 (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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200A THR* 3.4 21.9 + - - +
201A PRO 2.9 28.3 + - - -
202A PHE* 3.8 22.4 - - + +
203A PRO* 3.7 13.2 - - + +
206A SER* 5.2 1.1 - - - -
226A ALA* 1.3 78.6 - - - +
228A THR* 1.3 59.6 + - - +
229A ASN* 4.2 9.7 + - - +
231A PHE* 2.9 36.7 - - + -
249A LEU* 4.8 1.2 - - - +
294A ARG 3.8 0.5 - - - +
295A LEU* 3.6 3.3 - - - +
296A LEU* 2.7 34.7 + - + +
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Residues in contact with THR 228 (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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227A GLN* 1.3 73.3 + - - +
229A ASN* 1.3 70.7 + - - +
293A PRO* 5.4 4.0 - - + -
294A ARG 3.1 21.3 - - - +
295A LEU* 3.5 22.4 - - + +
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Residues in contact with ASN 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A THR* 4.3 25.9 - - - +
227A GLN* 4.6 8.7 - - - +
228A THR* 1.3 78.7 + - - +
230A LYS* 1.3 83.4 + - - +
231A PHE* 3.6 26.5 - - + -
291A ARG* 5.0 4.0 + - - -
293A PRO* 3.5 3.6 - - - +
294A ARG 2.8 30.1 + - - +
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Residues in contact with LYS 230 (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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229A ASN* 1.3 86.4 + - - +
231A PHE* 1.3 67.4 + - - +
291A ARG* 3.5 64.8 + - + +
292A LEU 3.2 4.5 - - - +
293A PRO* 3.7 34.6 - - + +
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Residues in contact with PHE 231 (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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200A THR* 4.1 12.3 - - - -
227A GLN* 2.9 37.9 - - + -
229A ASN* 3.6 35.0 - - + -
230A LYS* 1.3 79.0 - - - +
232A ASN* 1.3 64.8 - - - +
233A TYR* 3.4 4.0 + - - +
247A LEU* 3.7 27.4 - - + -
248A GLU 4.2 11.2 - - - +
249A LEU* 4.6 8.1 - - + -
250A PRO* 5.2 4.9 - - + -
290A THR 3.2 0.5 - - - +
291A ARG* 4.1 4.0 - - - +
292A LEU* 2.8 31.9 + - - +
294A ARG* 4.0 16.8 - - + +
296A LEU* 3.5 33.7 - - + -
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Residues in contact with ASN 232 (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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231A PHE* 1.3 72.1 - - - +
233A TYR* 1.3 59.5 + - - +
247A LEU* 3.5 5.0 - - - +
248A GLU* 3.0 65.3 + - + +
250A PRO* 5.6 4.2 - - - +
286A LYS* 4.2 8.3 - - - +
289A MET* 3.8 18.8 - - - +
290A THR* 3.6 19.4 + - - -
291A ARG* 3.8 20.1 + - - +
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Residues in contact with TYR 233 (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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231A PHE 4.0 7.4 - - - +
232A ASN* 1.3 76.9 - - - +
234A THR* 1.3 77.7 + - - +
235A GLU* 3.7 30.7 + - - +
243A TYR* 5.0 3.5 - - - -
245A ASP* 3.4 30.6 + - + +
246A ILE 3.4 14.4 - - - -
247A LEU* 4.8 4.0 - - + -
264A TYR* 5.9 2.8 - - - -
288A ASN 4.0 0.5 - - - +
289A MET* 3.1 9.5 - - - +
290A THR* 3.0 32.0 + - - +
292A LEU* 3.9 23.8 - - + -
294A ARG* 3.4 44.9 + - - -
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Residues in contact with THR 234 (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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233A TYR* 1.3 86.1 - - - +
235A GLU* 1.3 72.2 + - - +
236A PHE* 4.9 0.9 - - + +
245A ASP* 3.8 0.2 - - - -
246A ILE* 3.0 56.4 + - + +
285A TRP* 4.1 13.0 - - + +
288A ASN* 2.9 33.7 + - - +
289A MET* 3.8 16.6 - - + -
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Residues in contact with GLU 235 (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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233A TYR* 3.7 27.1 + - - +
234A THR* 1.3 82.2 + - - +
236A PHE* 1.3 60.6 + - - +
237A THR* 5.0 0.9 + - - -
243A TYR* 2.9 43.0 + - + +
244A TYR 3.7 4.0 - - - -
292A LEU* 5.9 0.7 - - - +
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Residues in contact with PHE 236 (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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234A THR* 4.0 1.9 - - + -
235A GLU* 1.3 73.4 - - - +
237A THR* 1.3 76.3 + - - +
238A THR* 3.5 18.2 - - + -
239A PRO* 5.1 1.6 - - + -
243A TYR* 3.3 5.7 - - - -
244A TYR* 2.7 50.0 + + + +
246A ILE* 3.9 19.5 - - + -
273A LEU* 3.3 34.1 - - + -
276A ILE* 3.6 18.6 - - + -
281A LEU* 3.8 24.2 - - + -
285A TRP* 3.8 18.6 - + + +
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Residues in contact with THR 237 (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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235A GLU 5.0 1.0 + - - -
236A PHE* 1.3 85.8 - - - +
238A THR* 1.3 66.9 + - - +
239A PRO* 3.7 2.6 - - - +
241A GLY* 3.9 10.3 - - - -
242A HIS 3.0 24.2 - - - +
243A TYR* 3.0 33.2 - - + -
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Residues in contact with THR 238 (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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236A PHE* 3.5 22.2 - - + -
237A THR* 1.3 75.5 - - - +
239A PRO* 1.3 59.7 - - - +
240A ASP* 2.6 23.9 + - - -
241A GLY* 2.6 31.5 + - - -
242A HIS* 2.8 27.9 + - - +
244A TYR* 3.4 22.7 - - + -
272A ALA* 3.5 18.9 - - - +
273A LEU* 3.8 4.3 - - + -
276A ILE* 3.8 7.0 - - + -
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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