Contacts of the strand formed by residues 322 - 335 (chain A) in PDB entry 5I2S
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 THR 322 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASN* 3.2 32.8 - - + +
318A ILE* 3.3 4.6 - - - -
319A ILE 2.9 34.8 + - - -
320A ASN* 3.4 1.6 + - - +
321A GLY* 1.3 80.5 + - - +
323A LEU* 1.3 70.9 + - - +
324A LYS* 3.6 9.7 + - - +
402A ALA* 4.3 2.9 - - - -
403A GLN* 3.6 13.9 + - - +
404A VAL* 5.7 0.4 - - - -
405A PHE* 3.9 22.4 - - + -
411A GLN* 4.1 7.3 + - - +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 3.9 0.7 - - - -
17A VAL* 3.5 45.7 + - + +
288A TRP* 3.6 15.0 - - + -
291A ILE* 3.5 33.4 - - + -
302A LEU* 4.0 24.5 - - + -
305A LEU* 5.1 0.9 - - + -
316A PHE* 4.6 6.3 - - + -
317A THR 3.6 16.4 - - - +
322A THR* 1.3 83.8 - - - +
324A LYS* 1.3 63.6 + - - +
402A ALA* 3.7 28.0 - - + +
403A GLN 3.1 9.9 + - - +
404A VAL* 4.0 3.7 - - + +
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 3.6 34.2 + - + +
15A LYS* 3.2 15.7 - - - +
16A ASN* 2.8 33.5 + - - +
17A VAL* 3.9 3.1 - - - -
316A PHE* 3.1 8.7 - - - +
317A THR* 2.9 38.5 + - + +
319A ILE* 4.1 29.6 - - + +
322A THR* 3.9 22.2 - - - +
323A LEU* 1.3 75.9 - - - +
325A TYR* 1.3 59.9 + - - +
411A GLN* 5.1 4.4 - - - +
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Residues in contact with TYR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 3.6 6.0 - - - -
15A LYS* 2.9 34.9 + - + +
16A ASN 3.7 18.6 - - - -
17A VAL* 3.5 20.4 - - + -
18A PRO* 4.9 1.1 - - + -
21A TYR* 4.0 11.7 - + - -
132A HIS* 3.4 12.7 + + - -
145A ASP* 2.4 36.6 + - - -
146A SER* 4.3 2.0 - - - -
147A GLN* 3.0 25.2 + - + +
314A PRO* 3.9 15.3 - - + -
315A ALA 2.8 15.0 - - - +
316A PHE* 3.5 19.7 - + + -
324A LYS* 1.3 71.7 - - - +
326A PHE* 1.3 81.6 + - - +
327A GLU* 3.9 15.7 - - - -
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Residues in contact with PHE 326 (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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7A PRO* 5.5 0.4 - - + -
9A ASN* 4.0 15.5 - - + -
11A LYS 4.2 2.7 - - - -
12A GLY* 3.6 22.4 - - - -
13A ASN* 3.3 31.9 - - + +
14A TRP* 3.5 31.2 - + - -
15A LYS* 4.1 11.4 - - + +
53A GLN* 5.1 8.5 - - - -
315A ALA* 2.9 47.2 + - + +
325A TYR* 1.3 88.7 - - - +
327A GLU* 1.3 70.8 + - - +
328A THR* 3.5 25.1 + - + -
357A TRP* 4.2 11.4 - + - -
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Residues in contact with GLU 327 (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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15A LYS* 5.3 2.6 - - - +
23A TYR* 5.4 1.0 + - - -
53A GLN* 5.5 1.0 - - - +
133A HIS 5.6 1.1 + - - +
134A VAL* 5.5 1.5 - - - -
135A LEU* 3.3 37.5 - - + +
144A VAL* 4.0 10.8 - - + +
145A ASP* 3.8 29.7 + - - +
146A SER* 2.2 42.5 + - - -
312A THR* 3.9 2.9 + - - -
313A GLY* 3.0 33.4 + - - +
314A PRO* 3.7 4.2 - - - +
325A TYR* 3.9 5.9 - - - -
326A PHE* 1.3 81.5 - - - +
328A THR* 1.3 59.2 - - - +
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Residues in contact with THR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.9 16.1 - - + +
8A HIS* 5.7 0.2 - - - -
9A ASN* 2.8 24.2 + - - -
135A LEU* 3.4 11.9 - - - +
312A THR* 3.2 5.2 - - - -
313A GLY 2.9 40.6 + - - +
315A ALA* 3.9 20.9 - - + -
326A PHE* 3.7 16.1 - - + -
327A GLU* 1.3 76.5 - - - +
329A ARG* 1.3 70.0 + - - +
330A TYR* 3.6 17.3 - - + -
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Residues in contact with ARG 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.4 2.1 - - - +
8A HIS* 2.9 49.4 + - + +
49A HIS 4.2 1.6 + - - -
50A LYS* 2.9 56.9 + - - +
52A ILE 4.6 0.6 + - - -
135A LEU* 3.9 23.7 - - + +
136A VAL 2.7 29.1 + - - +
137A ASP* 4.3 1.4 - - - +
138A GLU* 2.7 27.5 + - - +
144A VAL* 5.8 0.2 - - - +
311A GLY* 3.5 6.7 - - - +
312A THR* 3.8 28.2 - - + +
328A THR* 1.3 84.9 + - - +
330A TYR* 1.3 64.6 + - - +
331A ILE* 6.0 1.1 - - + -
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Residues in contact with TYR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 4.1 16.2 - - + -
6A PHE* 3.3 25.1 - - - +
7A PRO* 3.4 21.3 - - + -
208A ASN 4.4 0.7 - - - +
209A TYR* 4.8 2.4 - - - -
307A PRO* 3.2 31.5 - - + +
309A ASN 3.6 18.8 - - - +
310A PRO* 3.2 6.5 - - - +
311A GLY* 2.8 39.3 + - - +
313A GLY* 3.5 15.9 - - - -
314A PRO 2.5 30.8 + - - -
315A ALA* 3.3 7.3 - - - +
328A THR* 3.6 7.0 - - + -
329A ARG* 1.3 76.8 - - - +
331A ILE* 1.3 61.5 + - - +
371A ASN* 3.0 25.7 + - - -
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 3.1 7.3 - - - -
6A PHE* 2.9 40.3 + - + +
7A PRO 4.8 0.9 - - - +
8A HIS* 3.8 24.2 - - + -
208A ASN* 3.5 7.4 - - + +
209A TYR* 3.6 33.7 - - + +
329A ARG* 4.9 2.2 - - + +
330A TYR* 1.3 76.5 - - - +
332A ARG* 1.3 69.3 + - - +
333A VAL* 3.7 11.7 + - + +
347A ILE* 4.4 11.9 - - + -
354A ARG* 4.1 36.1 - - - +
356A LEU* 5.7 1.6 - - + -
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Residues in contact with ARG 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 3.5 25.1 - - + +
4A ILE 3.5 7.4 - - - +
5A VAL* 4.0 9.8 - - + +
29A ASP* 2.3 42.8 + - - -
30A LEU* 5.1 6.0 - - - +
206A ARG* 3.7 32.7 - - - +
207A SER 2.1 37.2 + - - -
208A ASN* 3.0 33.2 + - - +
210A PHE 4.2 0.6 + - - -
310A PRO* 3.6 17.7 - - + +
331A ILE* 1.3 75.8 - - - +
333A VAL* 1.3 59.9 + - - +
347A ILE* 3.9 10.6 - - - +
348A SER* 3.1 32.4 + - - -
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Residues in contact with VAL 333 (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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3A THR* 4.0 0.2 - - - +
4A ILE* 2.9 55.9 + - + +
6A PHE* 4.0 22.2 - - + -
331A ILE* 4.4 14.1 - - + +
332A ARG* 1.3 76.9 - - - +
334A ASP* 1.3 63.5 + - - +
335A ILE* 4.8 2.7 - - + -
345A GLY* 3.6 10.5 - - - +
346A MET 3.1 35.7 - - - +
347A ILE* 3.9 3.8 - - + +
348A SER 3.7 1.8 - - - +
354A ARG* 5.5 0.4 - - - -
356A LEU* 4.0 17.0 - - + -
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Residues in contact with ASP 334 (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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1A LYS* 3.7 14.8 + - + +
2A PHE 3.3 8.7 - - - +
3A THR* 2.7 31.0 + - - +
333A VAL* 1.3 71.6 - - - +
335A ILE* 1.3 60.3 + - - +
345A GLY* 3.5 2.1 - - - -
346A MET* 2.7 49.3 + - + +
348A SER* 2.9 19.9 + - - -
349A GLY* 3.2 21.5 + - - -
350A THR 4.7 3.6 - - - +
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Residues in contact with ILE 335 (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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1A LYS* 3.4 6.1 - - - +
2A PHE* 2.9 67.0 + - + +
4A ILE* 3.6 34.3 - - + -
333A VAL* 4.0 2.9 + - + -
334A ASP* 1.3 77.9 - - - +
336A ALA* 1.3 62.9 + - - +
337A ALA 3.9 9.6 - - - +
340A LEU* 4.2 12.3 - - + -
344A VAL 4.9 0.2 - - - -
345A GLY* 4.1 7.2 - - - -
356A LEU* 3.9 28.3 - - + -
382A PHE* 4.0 22.9 - - + -
385A TYR* 5.2 0.2 - - + -
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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