Contacts of the strand formed by residues 289 - 304 (chain A) in PDB entry 3U78
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 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PHE* 3.8 8.0 - - - -
287A GLY 3.8 0.4 + - - -
288A THR* 1.3 75.3 - - - +
290A VAL* 1.3 67.6 + - - +
348A VAL 3.2 15.7 - - - -
349A PRO 4.4 2.2 - - - -
350A THR* 3.5 12.6 + - - -
368A ASN* 3.3 1.0 - - - -
369A PHE* 3.0 53.3 + - - -
371A HIS* 2.8 28.9 - - - -
378A GLN* 5.5 0.4 + - - -
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 5.3 0.2 - - - -
284A ASP* 3.3 21.3 - - - +
289A SER* 1.3 71.7 - - - +
291A TRP* 1.3 63.7 + - - +
292A TYR* 3.7 32.3 - - + +
301A PHE* 5.9 0.2 - - + -
347A PHE* 3.3 7.3 - - - +
348A VAL* 2.8 56.0 + - + +
354A HIS* 5.4 2.0 - - - +
367A GLY 3.2 7.0 - - - +
368A ASN* 3.0 44.4 - - - +
369A PHE* 4.2 6.9 - - - -
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Residues in contact with TRP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 4.0 18.6 - - + -
239A VAL* 5.1 6.5 - - + -
241A VAL* 3.7 27.8 - - + +
242A PRO* 3.5 25.6 - - + +
245A ALA* 4.0 22.8 - - + +
267A GLN 3.9 2.6 + - - -
268A LYS* 5.4 0.7 - - - -
290A VAL* 1.3 76.6 - - - +
292A TYR* 1.3 74.6 + - - +
293A HIS* 4.0 13.7 - - + -
345A THR* 4.7 1.8 - - + -
346A LEU 3.2 7.0 - - - +
347A PHE* 3.5 28.3 - - + -
365A PHE* 3.3 26.9 - - + -
366A GLY* 3.0 47.7 - - - -
367A GLY* 3.2 26.1 + - - +
369A PHE* 4.4 2.5 - + - -
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Residues in contact with TYR 292 (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 ILE 5.2 2.1 + - - -
269A TYR* 5.9 3.3 - + + -
271A LEU* 3.6 36.4 - - + +
284A ASP* 5.0 0.9 - - - -
290A VAL* 3.7 35.7 - - + +
291A TRP* 1.3 85.4 - - - +
293A HIS* 1.3 60.1 + - - +
294A VAL* 6.1 1.6 - - + -
299A LYS* 5.6 2.5 - - + -
301A PHE* 3.8 35.9 - + + -
340A VAL* 5.0 4.8 - - + +
344A HIS 4.0 0.3 - - - +
345A THR* 3.3 5.2 - - - +
346A LEU* 2.7 40.5 + - + +
348A VAL* 5.5 1.6 - - + -
354A HIS* 5.5 0.7 - - - -
364A ALA* 5.0 5.8 - - + -
365A PHE 3.3 11.0 - - - -
366A GLY* 4.0 5.6 - - - -
367A GLY 5.5 0.9 - - - -
368A ASN* 4.8 4.3 + - - -
701A AKG 3.1 42.1 + - + -
702A NI 4.3 0.9 - - - +
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Residues in contact with HIS 293 (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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165A LEU* 3.8 26.1 - - + +
170A LEU* 3.3 18.1 - - + +
172A LEU* 3.6 28.0 - - + +
291A TRP* 4.0 7.2 - - + -
292A TYR* 1.3 73.2 - - - +
294A VAL* 1.3 79.4 + - - +
295A LEU* 3.6 8.0 + - + +
343A GLY* 3.3 31.1 - - - -
344A HIS 3.3 4.3 + - - -
345A THR* 2.8 23.1 + - - +
364A ALA* 3.0 5.8 - - - -
365A PHE* 2.7 41.3 + - - +
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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
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292A TYR* 5.7 1.6 - - + -
293A HIS* 1.3 78.5 + - - +
295A LEU* 1.3 58.1 + - - +
296A TRP 3.3 24.0 - - - +
297A GLY 3.5 20.0 - - - +
298A GLU 4.1 0.9 - - - +
299A LYS* 4.6 13.2 - - + +
301A PHE* 6.2 0.2 - - + -
340A VAL* 3.1 41.1 - - + +
341A LYS 3.7 9.2 - - - +
342A GLN* 4.2 4.0 - - - +
343A GLY 2.8 28.8 + - - -
344A HIS 3.7 4.2 + - - -
362A CYS* 3.6 12.3 - - - -
363A MET 3.9 2.5 - - - -
364A ALA* 4.1 4.3 - - + -
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Residues in contact with LEU 295 (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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172A LEU* 3.5 22.0 - - + -
173A PRO* 3.4 23.6 - - + +
174A SER 3.7 16.6 - - - +
175A PRO* 4.0 17.3 - - + +
177A PHE* 3.8 19.5 - - + -
293A HIS* 3.6 6.9 + - + +
294A VAL* 1.3 72.8 - - - +
296A TRP* 1.3 68.3 + - + +
342A GLN* 3.2 25.0 + - - +
343A GLY 4.7 0.2 + - - -
363A MET* 2.7 26.8 + - - +
365A PHE* 3.8 27.4 - - + -
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Residues in contact with TRP 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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175A PRO 3.3 22.9 - - - +
176A THR 4.8 0.8 - - - -
177A PHE 2.9 21.1 + - - -
178A SER* 4.7 2.4 - - - +
179A VAL* 4.6 9.9 - - + -
214A PHE* 4.1 22.9 - + - -
294A VAL* 3.3 2.6 - - - +
295A LEU* 1.3 84.8 - - + +
297A GLY* 1.3 65.5 + - - +
342A GLN* 3.9 18.8 - - - +
361A ASP* 3.2 43.1 - - + -
362A CYS* 3.2 12.9 - - - -
363A MET* 3.1 57.2 + - + +
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Residues in contact with GLY 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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294A VAL* 3.5 9.4 - - - +
296A TRP* 1.3 81.6 - - - +
298A GLU* 1.3 65.0 + - - +
342A GLN* 3.8 15.3 + - - +
360A GLN* 4.1 14.9 - - - +
361A ASP 3.1 22.5 + - - -
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Residues in contact with GLU 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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294A VAL* 4.3 1.1 - - - -
297A GLY* 1.3 77.6 - - - +
299A LYS* 1.3 66.7 + - - +
300A ILE* 4.2 5.4 - - - +
339A VAL* 3.7 23.6 - - + +
340A VAL 3.7 13.9 - - - +
341A LYS* 3.7 24.4 - - + +
358A THR* 3.9 2.1 - - - -
359A SER* 2.9 45.3 + - - +
360A GLN* 3.6 34.6 + - - +
362A CYS* 3.8 6.7 - - - +
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Residues in contact with LYS 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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224A ASN* 5.1 3.8 + - - -
226A ILE* 6.3 0.2 - - - -
271A LEU* 4.1 21.5 - - + -
272A MET 6.2 0.4 - - - -
273A GLY* 5.6 2.3 - - - +
292A TYR* 5.6 3.6 - - + -
294A VAL* 4.6 8.2 - - + +
298A GLU* 1.3 74.2 - - - +
300A ILE* 1.3 66.5 + - - +
301A PHE* 4.0 23.3 - - + -
340A VAL* 2.8 34.7 + - + +
356A VAL* 4.1 6.9 - - + +
357A LEU 3.4 5.8 - - - +
358A THR* 2.8 34.1 + - - +
362A CYS* 3.7 26.4 - - - +
364A ALA* 4.2 13.0 - - + -
701A AKG 3.2 27.1 + - - +
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Residues in contact with ILE 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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127A ARG* 5.7 1.8 - - - +
298A GLU* 4.2 10.3 - - - +
299A LYS* 1.3 80.5 - - - +
301A PHE* 1.3 63.1 + - - +
302A TYR* 3.3 31.3 - - + +
337A LYS* 3.9 32.1 - - + -
338A CYS 3.4 7.2 - - - +
339A VAL* 4.3 13.5 - - + -
356A VAL* 3.4 0.7 - - - -
357A LEU* 2.8 50.9 + - + +
359A SER* 3.7 30.5 - - - +
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Residues in contact with PHE 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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292A TYR* 3.8 45.1 - + + -
299A LYS* 4.0 27.1 - - + -
300A ILE* 1.3 78.9 - - - +
302A TYR* 1.3 61.2 + - - +
303A LEU* 3.9 23.6 - - + -
336A TYR 3.3 1.9 - - - +
337A LYS* 3.5 2.4 - - - -
338A CYS* 2.7 39.6 + - - +
340A VAL* 3.9 24.0 - - + -
346A LEU* 4.0 17.0 - - + -
348A VAL* 4.8 4.7 - - + -
354A HIS* 4.3 15.9 - + - -
355A ALA 3.5 4.5 - - - +
356A VAL* 3.8 25.1 - - + -
701A AKG 5.1 1.8 - - + -
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Residues in contact with TYR 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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126A LEU* 3.5 34.4 + - + +
127A ARG* 5.6 0.2 - - - -
131A PHE* 3.6 46.2 - + - -
281A PHE* 3.6 16.1 - + + -
300A ILE* 3.3 36.6 - - + +
301A PHE* 1.3 74.3 - - - +
303A LEU* 1.3 60.3 + - - +
327A PHE* 5.3 0.2 - + - -
335A CYS* 3.8 14.6 - - - -
336A TYR 3.2 4.9 - - - -
337A LYS* 4.4 10.7 - - + +
354A HIS* 2.9 25.6 - - - -
355A ALA* 2.9 23.1 + - + +
356A VAL 4.5 0.4 - - - -
357A LEU* 3.5 29.7 - - + +
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Residues in contact with LEU 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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134A ALA* 4.5 7.9 - - + -
137A ILE* 5.3 0.9 - - + -
138A ILE* 5.0 0.9 - - + -
159A PRO* 4.3 19.7 - - + -
301A PHE* 4.0 14.4 - - + -
302A TYR* 1.3 74.1 - - - +
304A ILE* 1.3 65.5 + - - +
305A LYS 4.2 0.2 - - - -
335A CYS* 3.6 0.9 - - - -
336A TYR* 2.7 51.8 + - + +
338A CYS* 3.7 32.3 - - + -
346A LEU* 4.7 3.4 - - + -
348A VAL* 4.2 28.7 - - + -
352A TRP* 4.0 17.5 - - + -
353A ILE 3.5 2.0 - - - +
354A HIS* 3.7 21.1 - - + -
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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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281A PHE* 3.6 22.4 - - + -
303A LEU* 1.3 80.7 - - - +
305A LYS* 1.3 68.1 + - - +
306A PRO 3.5 0.3 - - - -
310A ASN* 3.5 30.3 - - + +
328A PHE* 3.6 30.5 - - + -
329A GLY* 4.3 1.8 - - - -
332A VAL* 3.7 20.6 - - + -
334A LYS 3.9 12.3 - - - +
335A CYS* 4.1 12.6 - - - -
352A TRP* 3.4 7.9 - - - -
353A ILE* 2.7 45.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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