Contacts of the strand formed by residues 3 - 15 (chain D) in PDB entry 5U0A
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 PHE 3 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D THR* 1.3 88.8 - - - +
4D VAL* 1.3 62.4 + - - +
5D ASP* 3.7 1.1 + - - -
236D ASN* 4.1 10.3 - - - +
237D VAL 3.3 3.8 - - - +
238D ASN* 2.7 47.3 - - - -
240D ASP* 5.5 0.7 - - - -
241D ARG* 6.2 0.9 - - - -
287D ALA 3.6 2.1 - - - +
288D VAL* 4.7 0.9 - - - -
289D ARG* 2.8 41.8 + - + +
290D PHE 5.2 2.5 - - - -
291D ASP 4.5 2.7 - - - -
292D ARG* 4.0 6.7 - - - -
293D PRO* 3.1 42.8 - - + -
132N PRO* 3.7 38.1 - - + -
133N TYR 4.6 2.5 - - - -
135N GLN* 3.8 9.6 - - + -
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Residues in contact with VAL 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D THR* 5.0 0.7 - - + -
3D PHE* 1.3 73.7 - - - +
5D ASP* 1.3 59.2 + - - +
6D ILE* 5.4 1.4 - - - +
235D ALA 4.9 0.2 - - - -
236D ASN* 3.7 1.1 - - - -
237D VAL* 2.9 45.8 + - + +
239D LEU* 4.0 28.0 - - + -
256D VAL* 5.0 9.6 - - + -
260D LEU* 4.7 16.8 - - + +
286D ILE* 3.7 28.3 - - + -
287D ALA 4.3 1.6 - - - -
288D VAL* 4.0 23.6 - - + +
363D MET* 5.1 4.0 - - + +
364D VAL* 6.5 0.2 - - + -
367D ALA* 4.6 5.4 - - + -
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Residues in contact with ASP 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D PHE 4.9 1.6 - - - -
4D VAL* 1.3 74.8 - - - +
6D ILE* 1.3 62.4 + - - +
7D HIS* 3.7 10.1 + - - -
234D TYR* 3.3 15.1 + - + +
235D ALA 3.2 14.8 - - - +
236D ASN* 4.2 7.4 - - + +
285D HIS 3.8 1.0 - - - +
286D ILE* 3.4 5.0 - - - +
287D ALA* 2.6 46.5 + - - +
289D ARG* 4.1 11.6 - - - -
293D PRO* 4.9 3.6 - - + -
294D ILE* 3.2 30.8 + - - +
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Residues in contact with ILE 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL 5.4 0.9 - - - +
5D ASP* 1.3 78.0 - - - +
7D HIS* 1.3 70.6 + - - +
234D TYR* 3.3 5.1 - - - -
235D ALA* 2.9 44.9 + - + +
237D VAL* 6.2 1.6 - - + -
259D PHE* 5.6 2.0 - - + -
260D LEU* 4.5 21.5 - - + +
263D PHE* 3.7 37.3 - - + -
264D LEU* 3.9 21.3 - - + -
284D VAL* 4.8 3.4 - - + -
285D HIS 3.4 4.9 - - - +
286D ILE* 3.9 34.1 - - + -
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Residues in contact with HIS 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ASP* 3.7 18.6 - - - -
6D ILE* 1.3 75.2 - - - +
8D ALA* 1.3 60.7 + - - +
9D ILE* 5.8 0.7 - - + -
232D TYR* 2.5 43.5 + + + -
233D ARG 3.6 4.5 - - - -
234D TYR* 3.2 30.9 - + - -
283D LEU* 3.6 3.1 - - + +
284D VAL* 3.1 5.7 - - - +
285D HIS* 2.9 50.3 + + + +
287D ALA* 5.5 2.0 - - + -
294D ILE* 3.3 10.5 + - + -
296D PHE* 3.5 34.2 + + - -
318D LEU* 5.0 6.3 - - + -
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Residues in contact with ALA 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE 4.3 0.4 + - - -
7D HIS* 1.3 74.8 - - - +
9D ILE* 1.3 64.6 + - - +
10D GLN 3.6 1.6 + - - +
232D TYR* 3.6 3.2 - - - -
233D ARG* 2.8 45.3 + - + +
263D PHE* 4.2 20.2 - - + -
264D LEU* 4.7 0.7 - - + -
281D PRO* 4.0 22.7 - - + -
283D LEU 3.0 10.3 - - - +
284D VAL* 4.3 6.3 - - + -
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Residues in contact with ILE 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D HIS 5.8 0.7 - - - -
8D ALA* 1.3 74.6 - - - +
10D GLN* 1.3 57.5 - - - +
194D VAL* 4.7 3.6 - - + -
230D THR* 3.4 26.5 - - + -
231D PHE 3.7 5.2 - - - +
232D TYR* 4.3 11.9 - - + -
281D PRO* 4.6 0.2 - - - -
282D ASP* 3.1 31.0 + - + +
283D LEU* 2.9 29.5 + - + -
300D PHE* 4.2 6.5 - - + -
311D THR* 5.2 5.4 - - - +
314D ALA* 3.8 39.7 - - + +
315D CYS* 4.2 9.0 - - - +
318D LEU* 4.2 19.1 - - + -
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Residues in contact with GLN 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ALA 3.6 1.6 - - - -
9D ILE* 1.3 73.9 - - - +
11D THR* 1.3 68.8 + - - +
12D LEU* 4.2 12.7 - - + +
43D TRP* 3.9 6.2 - - - -
230D THR* 4.4 0.4 - - - -
231D PHE* 2.9 34.5 + - - +
233D ARG* 3.2 41.1 + - - +
264D LEU 4.5 1.4 + - - +
266D THR 4.4 1.6 + - - -
267D VAL* 3.3 22.8 - - - +
279D THR 3.1 25.8 + - - -
280D LEU 4.1 2.5 - - - -
281D PRO* 3.5 37.8 - - + +
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Residues in contact with THR 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE 3.9 1.2 + - - -
10D GLN* 1.3 76.5 - - - +
12D LEU* 1.3 78.3 + - - +
13D PRO* 4.2 0.6 - - - +
229D GLY 3.3 12.2 + - - -
230D THR* 3.4 24.0 + - - +
279D THR* 3.5 16.6 - - + +
280D LEU 5.1 0.8 + - - +
282D ASP* 3.4 22.6 + - - +
311D THR* 4.7 4.9 - - + -
30H TYR* 4.3 13.4 + - - +
298H PRO* 3.6 31.0 - - + -
301H GLU* 4.6 3.7 - - + +
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLN* 4.2 15.9 - - + +
11D THR* 1.3 87.3 + - - +
13D PRO* 1.3 75.6 - - + +
15D SER* 4.1 7.6 - - - +
17D ILE* 3.6 24.7 - - + -
38D VAL* 5.0 0.4 - - + -
43D TRP* 5.2 8.5 - - + -
228D ALA* 3.3 2.0 - - - +
229D GLY 2.8 36.6 + - - +
231D PHE* 3.4 37.7 - - + -
267D VAL* 4.7 3.8 - - + -
277D ALA* 3.3 29.6 - - + +
279D THR* 3.8 7.2 - - - +
30H TYR* 4.3 1.7 - - - -
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Residues in contact with PRO 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D THR 4.2 1.8 - - - +
12D LEU* 1.3 90.6 - - + +
14D TYR* 1.3 60.7 + - + +
15D SER* 2.8 28.6 + - - -
227D SER 3.7 0.3 - - - +
228D ALA* 3.4 8.0 - - + +
276D ALA 4.4 6.5 - - - +
277D ALA* 4.3 18.4 - - - +
279D THR* 3.7 19.7 - - + +
30H TYR* 4.0 15.7 - - + +
192H PHE* 4.7 10.3 - - + -
295H SER* 4.7 1.1 - - - +
297H ALA* 4.0 29.8 - - + -
298H PRO* 5.1 1.3 - - + -
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Residues in contact with TYR 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D PRO* 1.3 74.8 - - + +
15D SER* 1.3 59.6 + - - +
200D GLU* 3.1 34.8 + - + -
202D ASP* 3.0 17.5 - - - +
226D PHE* 3.0 35.5 - + + +
227D SER 3.9 1.1 - - - -
228D ALA* 3.4 10.9 - - - +
275D THR* 3.2 19.9 - - - -
276D ALA 5.9 0.2 - - - -
277D ALA* 5.2 0.7 - - - +
27H THR 5.1 0.7 - - - -
28H VAL* 3.6 24.8 - - + +
30H TYR* 5.2 1.0 - - - -
37H ARG* 2.7 36.9 + - - -
190H HIS* 3.3 50.3 + + + +
192H PHE* 6.0 4.6 - - + -
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Residues in contact with SER 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.1 12.5 - - - +
13D PRO 2.8 13.2 + - - -
14D TYR* 1.3 78.6 - - - +
16D ASN* 1.3 62.2 + - - +
17D ILE* 3.9 12.1 + - - +
226D PHE* 3.5 4.2 - - - -
227D SER* 2.7 36.7 + - - +
231D PHE* 5.9 1.4 - - - -
272D GLN* 5.3 0.2 - - - -
275D THR* 3.5 21.1 - - - -
277D ALA* 3.6 18.3 - - - +
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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