Contacts of the strand formed by residues 298 - 308 (chain A) in PDB entry 2EC8
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 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A VAL* 2.7 22.7 - - - +
212A PRO* 4.2 0.2 - - - -
291A TYR* 3.1 33.9 + - - -
292A ALA 3.0 15.9 - - - -
293A ASN* 3.2 11.0 - - - +
297A GLY* 1.3 72.6 - - - -
299A ALA* 1.3 57.9 + - - +
300A ASN* 5.7 0.3 + - - -
800A NAG 4.2 5.4 + - - -
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Residues in contact with ALA 299 (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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211A VAL* 3.7 10.1 - - + -
212A PRO* 3.3 28.5 - - + +
214A VAL* 4.0 11.5 - - + +
290A CYS 3.8 0.5 - - - +
291A TYR* 3.5 1.9 - - - -
292A ALA* 2.6 43.0 + - + +
298A SER* 1.3 76.4 + - - +
300A ASN* 1.3 59.7 + - - +
800A NAG 5.9 0.4 - - - -
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Residues in contact with ASN 300 (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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214A VAL* 4.1 0.6 - - - +
289A MET* 3.5 26.9 - - + +
290A CYS 3.0 9.2 - - - +
291A TYR* 4.2 7.0 - - + -
298A SER* 5.7 0.2 + - - -
299A ALA* 1.3 76.7 - - - +
301A VAL* 1.3 69.3 + - - +
302A THR* 5.2 1.6 + - - -
800A NAG 1.6 71.1 + - - +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A VAL* 3.0 44.2 - - + +
215A SER* 4.7 0.9 - - - -
216A VAL* 4.1 31.7 - - + +
219A ALA* 6.2 1.6 - - + -
288A PHE 4.2 0.5 - - - +
289A MET* 3.7 1.1 - - - -
290A CYS* 2.8 36.0 + - + +
300A ASN* 1.3 78.0 - - - +
302A THR* 1.3 69.1 + - - +
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Residues in contact with THR 302 (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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216A VAL* 5.0 0.4 - - - +
219A ALA* 4.0 14.2 - - - +
249A GLU* 5.3 0.4 + - - -
287A VAL* 2.7 37.4 - - + +
288A PHE 3.8 4.3 + - - -
289A MET* 4.4 10.2 - - - +
300A ASN* 5.2 1.8 + - - -
301A VAL* 1.3 84.8 - - - +
303A THR* 1.3 59.6 + - - +
304A THR* 4.6 4.4 - - + +
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Residues in contact with THR 303 (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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216A VAL* 4.3 8.1 - - + -
218A LYS 3.1 23.1 + - - -
219A ALA* 3.3 12.5 + - - -
221A TYR* 3.7 15.6 - - + -
229A PHE* 5.6 1.1 - - + -
231A VAL* 4.6 9.0 - - + -
246A TRP* 3.9 18.6 - - + -
286A GLY 4.1 0.2 - - - +
288A PHE* 2.9 50.8 + - + +
302A THR* 1.3 77.4 + - - +
304A THR* 1.3 61.9 + - - +
305A LEU* 4.1 0.5 + - - +
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Residues in contact with THR 304 (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 ALA 3.3 7.3 + - - +
220A SER* 3.4 15.2 + - - -
221A TYR 3.0 23.6 + - - +
286A GLY 3.8 7.2 - - - -
287A VAL* 3.7 26.9 - - + +
302A THR* 4.6 5.6 - - + +
303A THR* 1.3 75.3 + - - +
305A LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 305 (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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221A TYR* 3.5 29.4 - - + +
223A LEU* 3.8 32.3 - - + -
229A PHE* 4.1 22.0 - - + -
277A ILE* 6.0 0.2 - - + -
284A ASP* 4.5 5.2 - - + -
285A SER* 3.1 27.4 - - - +
286A GLY* 3.0 35.2 + - - +
288A PHE* 4.2 20.2 - - + -
303A THR* 5.8 0.2 - - - +
304A THR* 1.3 77.9 - - - +
306A GLU* 1.3 63.6 + - - +
307A VAL* 3.6 14.4 - - + -
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Residues in contact with GLU 306 (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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221A TYR 3.1 13.4 + - - +
222A LEU* 4.5 11.3 - - + +
223A LEU 2.7 30.7 + - - +
285A SER* 3.7 6.7 - - - -
305A LEU* 1.3 74.6 - - - +
307A VAL* 1.3 57.3 + - - +
308A VAL* 4.1 13.5 + - + +
371A ILE* 6.1 0.7 - - - +
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Residues in contact with VAL 307 (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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223A LEU* 3.5 18.2 - - + -
224A ARG 4.0 3.1 - - - -
225A GLU* 3.4 33.0 - - + +
280A ALA* 4.1 14.6 - - + +
281A ARG 3.8 11.0 - - - +
282A VAL* 3.5 42.4 - - - +
284A ASP* 4.7 1.6 - - + -
285A SER* 3.8 8.3 + - - +
305A LEU* 3.6 25.6 - - + -
306A GLU* 1.3 71.4 - - - +
308A VAL* 1.3 65.2 + - - +
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Residues in contact with VAL 308 (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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223A LEU 2.7 14.9 + - - +
224A ARG* 3.1 9.4 - - - +
225A GLU* 2.8 20.9 + - - -
282A VAL* 4.6 1.1 - - - -
306A GLU* 5.0 16.4 - - + +
307A VAL* 1.3 80.8 - - - +
309A ASP* 1.3 64.3 + - - +
310A LYS* 3.0 31.1 - - + +
312A PHE* 4.7 19.1 - - + -
340A PHE* 4.7 11.1 - - + -
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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