Contacts of the strand formed by residues 293 - 304 (chain A) in PDB entry 1H6T
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 GLU 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A LEU* 5.6 0.2 - - - +
274A ASP* 4.1 2.8 - - - +
291A THR* 3.4 17.1 - - - +
292A ASN* 1.3 79.6 - - - +
294A VAL* 1.3 66.8 + - - +
295A SER* 5.8 0.4 - - - -
316A THR* 3.5 31.1 - - + +
317A GLN 3.4 16.6 - - - +
318A PRO* 4.1 14.5 - - + +
319A LEU* 3.8 3.2 - - - +
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.7 23.3 - - + -
273A SER* 3.5 9.0 - - - +
274A ASP* 3.7 13.9 - - - +
285A TRP* 3.5 35.9 - - + +
287A LEU* 3.7 28.3 - - + -
293A GLU* 1.3 81.8 - - - +
295A SER* 1.3 65.4 + - - +
316A THR* 3.7 0.3 - - - -
317A GLN* 2.8 44.0 + - + +
319A LEU* 4.8 1.8 - - + +
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A SER* 2.9 38.2 + - - -
285A TRP* 3.8 5.8 - - - -
293A GLU* 5.8 0.7 - - - -
294A VAL* 1.3 79.4 - - - +
296A PHE* 1.3 69.9 + - - +
297A ILE* 6.0 0.3 - - - +
314A ARG* 4.1 21.2 - - - -
315A VAL 3.1 15.5 - - - -
316A THR* 4.1 7.0 - - - -
317A GLN* 4.7 0.7 - - - +
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Residues in contact with PHE 296 (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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255A VAL* 4.1 16.8 - - + -
256A PRO 5.1 0.7 - - - -
257A ASN* 4.2 24.9 - - - -
258A THR* 5.5 1.1 - - - -
259A VAL* 4.5 4.5 - - + -
269A PRO* 3.9 22.9 - - + -
271A ILE 3.3 13.2 - - - +
272A ILE* 4.0 15.3 - - + -
273A SER 4.7 0.2 - - - +
283A VAL* 3.9 21.8 - - + -
285A TRP* 4.2 14.6 - + - -
295A SER* 1.3 80.4 - - - +
297A ILE* 1.3 71.7 + - - +
298A PHE* 4.7 2.9 - - + -
314A ARG* 3.3 4.1 - - - -
315A VAL* 2.9 75.0 + - + +
317A GLN* 6.4 0.9 - - + -
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Residues in contact with ILE 297 (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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269A PRO* 3.7 4.5 - - - +
270A GLU* 2.7 56.2 + - + +
271A ILE* 2.9 21.7 + - + +
295A SER* 6.0 0.4 - - - +
296A PHE* 1.3 76.8 - - - +
298A PHE* 1.3 64.8 + - - +
312A HIS* 3.8 22.2 - - + +
313A GLY 3.2 8.1 - - - +
314A ARG* 3.5 39.5 - - + +
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Residues in contact with PHE 298 (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 ILE 3.8 19.5 - - - -
240A GLN* 4.0 3.4 - - + -
242A CYS* 4.3 9.9 - - - -
259A VAL* 3.7 40.6 - - + -
267A VAL* 4.3 10.3 - - + +
269A PRO* 4.5 6.3 - - + -
270A GLU 4.1 4.0 - - - +
296A PHE* 4.9 4.5 - - + -
297A ILE* 1.3 79.8 - - - +
299A TYR* 1.3 64.3 + - - +
311A PHE* 3.5 37.2 - + - -
312A HIS* 3.3 8.2 - - - -
313A GLY* 2.8 56.7 + - - +
314A ARG* 3.9 3.1 - - - -
315A VAL* 4.1 16.4 - - + -
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Residues in contact with TYR 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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267A VAL* 3.4 14.5 - - - +
268A THR 4.3 5.5 + - - +
270A GLU* 3.4 33.4 - - + +
298A PHE* 1.3 76.8 - - - +
300A GLN* 1.3 63.8 + - - +
301A PRO* 3.6 40.1 - - + +
308A LYS* 4.8 5.9 + - - -
309A ALA 4.5 0.5 + - - -
310A ARG* 3.7 48.0 - - + +
311A PHE 3.2 11.7 - - - -
312A HIS* 4.0 13.7 - + + -
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Residues in contact with GLN 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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261A ASN* 3.6 38.8 - - - +
266A LEU 5.2 0.5 - - - +
267A VAL* 3.7 35.0 - - + +
268A THR 5.1 0.7 + - - -
299A TYR* 1.3 80.9 - - - +
301A PRO* 1.3 94.8 + - - +
302A VAL* 4.4 2.0 - - + -
311A PHE* 2.8 46.3 + - + +
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Residues in contact with PRO 301 (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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261A ASN* 5.0 1.6 + - - -
299A TYR* 3.6 33.6 - - + +
300A GLN* 1.3 107.8 + - - +
302A VAL* 1.3 60.1 + - - +
303A THR* 4.3 0.4 + - - -
308A LYS* 3.8 18.2 - - - +
309A ALA 3.7 3.1 - - - +
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Residues in contact with VAL 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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223A LEU* 3.6 26.0 - - + -
235A LEU* 4.1 11.7 - - + -
237A LEU* 4.5 4.0 - - + -
261A ASN* 4.3 9.4 - - - +
262A THR* 4.5 9.0 - - + +
300A GLN* 3.7 12.1 - - + +
301A PRO* 1.3 77.7 - - - +
303A THR* 1.3 64.8 + - - +
304A ILE* 3.7 32.8 - - + -
307A ALA 3.7 0.3 - - - +
308A LYS* 3.3 7.5 - - - +
309A ALA* 2.8 46.4 + - + +
311A PHE* 3.8 7.4 - - + -
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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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262A THR* 5.6 1.4 + - - -
301A PRO 4.2 1.3 + - - -
302A VAL* 1.3 76.0 + - - +
304A ILE* 1.3 68.6 + - - +
305A GLY 3.8 19.2 + - - +
306A LYS 5.6 0.2 - - - -
307A ALA 3.3 7.6 - - - +
308A LYS* 4.4 14.3 - - + +
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Residues in contact with ILE 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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226A LEU* 3.7 38.1 - - + +
227A ALA 4.2 10.5 - - - +
229A LEU 3.1 32.5 - - - +
230A LYS* 4.4 1.8 - - - +
232A LEU* 3.7 13.7 - - + +
235A LEU* 3.9 15.3 - - + -
262A THR* 4.0 13.0 - - + +
302A VAL* 3.7 23.3 - - + +
303A THR* 1.3 78.6 - - - +
305A GLY* 1.3 66.4 + - - +
306A LYS 3.2 0.5 + - - -
307A ALA* 3.0 25.8 + - + +
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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