Contacts of the helix formed by residues 320 - 333 (chain A) in PDB entry 2I91
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 HIS 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLY 3.5 11.1 + - - +
85A ARG 3.0 26.9 - - - -
86A ALA 4.8 0.9 - - - +
87A ALA* 3.4 26.6 + - + +
318A ARG 3.2 7.1 + - - +
319A ILE* 1.3 75.0 - - - +
321A PRO* 1.3 75.7 - - + +
322A PHE* 3.1 36.3 - - + -
323A HIS* 3.2 34.8 + - + +
324A ILE* 3.4 11.8 + - - +
522A PHE* 3.2 30.3 + - - -
524A SER* 3.5 18.0 + - - -
13D C 6.2 0.7 - - - +
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Residues in contact with PRO 321 (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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320A HIS* 1.3 108.0 - - + +
322A PHE* 1.3 58.3 + - - +
324A ILE* 3.0 8.6 + - + +
325A LEU 2.8 24.6 + - - -
357A PHE* 3.5 14.4 - - + -
360A SER* 3.5 25.3 - - - +
361A PHE* 3.4 48.0 - - + -
522A PHE* 3.6 4.7 - - + -
524A SER* 4.1 10.8 - - - -
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Residues in contact with PHE 322 (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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87A ALA* 3.6 17.3 - - + -
88A LYS* 4.5 11.9 - - - -
320A HIS* 3.1 13.1 - - + -
321A PRO* 1.3 75.7 - - - +
323A HIS* 1.3 82.2 - + - +
325A LEU* 3.0 4.7 + - - +
326A VAL* 2.8 50.5 + - + +
385A VAL* 4.5 3.4 - - + -
386A LEU* 3.7 34.5 - - + -
388A SER* 3.6 26.2 - - - -
390A LEU* 4.6 8.5 - - + -
395A VAL* 5.6 5.2 - - + -
522A PHE* 3.0 33.1 - + + -
10D U 5.6 4.3 - - - -
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Residues in contact with HIS 323 (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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87A ALA 2.8 28.8 + - - -
88A LYS* 4.7 0.4 - - + -
279A THR* 5.9 7.2 - - + -
282A LEU* 3.9 18.1 - - + +
318A ARG 5.1 2.5 - - - -
319A ILE* 4.9 3.1 - - + -
320A HIS* 3.2 34.0 + - + +
322A PHE* 1.3 101.6 - + - +
324A ILE* 1.3 61.6 + - - +
326A VAL* 4.0 4.5 - - - +
327A ALA* 3.2 24.4 + - - +
9D U 4.8 1.6 - - - +
10D U 5.0 1.8 - - - -
11D U 3.8 20.0 - - - -
13D C 6.0 5.4 - + - -
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Residues in contact with ILE 324 (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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282A LEU* 3.7 19.3 - - + -
308A LEU* 5.8 1.3 - - + -
314A LEU* 4.9 4.3 - - + -
319A ILE* 3.2 29.2 - - + -
320A HIS 3.4 13.2 - - - +
321A PRO* 3.0 12.1 + - + +
323A HIS* 1.3 74.3 - - - +
325A LEU* 1.3 62.8 + - - +
327A ALA* 3.2 3.8 + - - +
328A LEU* 2.8 30.5 + - + +
353A LEU* 3.4 37.6 - - + +
356A ALA* 4.5 11.9 - - + -
357A PHE* 3.8 17.5 - - + +
360A SER* 4.0 10.5 - - - +
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Residues in contact with LEU 325 (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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321A PRO 2.8 12.4 + - - +
322A PHE* 3.0 8.9 + - - +
324A ILE* 1.3 77.7 - - - +
326A VAL* 1.3 62.1 + - - +
328A LEU* 3.2 6.7 + - + +
329A GLU* 2.9 25.3 + - + +
357A PHE* 4.1 7.6 - - + -
390A LEU* 3.2 40.4 - - + -
394A VAL* 4.4 9.9 - - + -
395A VAL* 4.3 18.6 - - + -
398A ALA* 4.4 14.8 - - + -
430A LEU* 4.2 17.7 - - + -
434A VAL* 4.5 15.3 - - + -
522A PHE* 4.4 10.3 - - + -
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Residues in contact with VAL 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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322A PHE* 2.8 57.3 + - + +
323A HIS* 4.0 5.6 - - - +
325A LEU* 1.3 72.3 - - - +
327A ALA* 1.3 57.8 + - - +
329A GLU* 3.8 3.6 - - - +
330A THR* 3.0 29.4 + - - +
388A SER* 4.2 9.9 - - - -
389A ILE* 6.0 2.2 - - + +
390A LEU* 3.7 15.3 - - + -
9D U 3.6 17.9 - - - +
10D U 3.2 26.5 - - - +
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Residues in contact with ALA 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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282A LEU* 4.1 20.9 - - + +
285A LEU* 5.3 0.4 - - + -
323A HIS 3.2 14.5 + - - +
324A ILE 3.2 4.4 + - - +
326A VAL* 1.3 76.2 - - - +
328A LEU* 1.3 61.6 + - - +
331A TYR* 2.7 36.3 + - - +
353A LEU* 4.2 5.6 - - + -
9D U 3.2 37.7 + - + +
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Residues in contact with LEU 328 (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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324A ILE* 2.8 23.4 + - + +
325A LEU* 3.7 7.0 - - + +
327A ALA* 1.3 74.1 - - - +
329A GLU* 1.3 67.3 + - - +
331A TYR* 3.9 0.3 - - - +
332A LYS* 3.0 30.9 + - + +
350A VAL* 3.7 13.9 - - + +
353A LEU* 3.7 20.3 - - + +
354A ASP* 3.2 47.1 - - + +
357A PHE* 6.2 0.2 - - + -
430A LEU* 4.6 11.0 - - + -
431A HIS* 3.5 39.7 - - + +
434A VAL* 5.4 3.4 - - + -
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Residues in contact with GLU 329 (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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325A LEU* 2.9 21.4 + - + +
326A VAL* 3.8 5.2 - - - +
328A LEU* 1.3 78.5 - - - +
330A THR* 1.3 62.3 + - - +
332A LYS* 2.8 46.9 + - - +
333A LYS* 2.7 42.3 + - - +
389A ILE* 5.2 10.6 - - + +
390A LEU* 3.9 24.9 - - + -
434A VAL* 3.8 22.1 - - + +
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Residues in contact with THR 330 (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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326A VAL* 3.0 18.7 + - - +
327A ALA 4.2 0.2 - - - -
329A GLU* 1.3 75.5 - - - +
331A TYR* 1.3 66.6 + - - +
333A LYS* 3.2 22.2 + - + +
335A HIS 3.4 5.5 - - - +
336A GLY* 3.8 24.0 - - - -
337A ASN* 4.5 2.6 + - - +
343A TRP* 3.5 6.2 - - + -
389A ILE* 5.2 8.1 - - - +
9D U 3.5 56.0 + - + +
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Residues in contact with TYR 331 (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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285A LEU* 3.7 20.6 - - + -
286A GLY* 3.7 14.8 - - - -
289A THR* 2.7 30.1 + - - +
327A ALA 2.7 26.1 + - - +
328A LEU* 3.9 2.5 - - - +
330A THR* 1.3 74.6 - - - +
332A LYS* 1.3 61.9 + - - +
334A GLY 3.2 2.9 + - - -
343A TRP* 2.7 45.3 + + - -
345A PRO* 3.5 8.6 - - + +
346A ASP* 3.2 40.7 + - - +
349A ILE* 3.5 36.2 - - + +
350A VAL* 4.0 13.0 - - + -
353A LEU* 4.3 9.2 - - + -
9D U 4.1 5.8 - - + +
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Residues in contact with LYS 332 (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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328A LEU* 3.0 18.2 + - + +
329A GLU* 2.8 42.1 + - - +
331A TYR* 1.3 72.2 - - - +
333A LYS* 1.3 59.1 + - + +
334A GLY 3.0 9.8 + - - -
345A PRO* 3.7 21.4 - - + +
350A VAL* 4.4 17.3 - - + -
431A HIS* 2.8 71.5 + - + +
434A VAL* 4.4 3.6 - - - +
435A GLU* 5.1 5.5 + - - +
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Residues in contact with LYS 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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329A GLU* 2.7 41.0 + - - +
330A THR* 3.2 17.2 + - + +
331A TYR 3.1 1.2 - - - -
332A LYS* 1.3 81.9 - - + +
334A GLY* 1.3 51.4 + - - +
335A HIS* 2.7 55.5 + - + +
336A GLY 5.8 1.6 - - - +
337A ASN* 6.4 2.0 - - + -
389A ILE* 5.7 5.9 - - - +
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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