Contacts of the helix formed by residues 320 - 332 (chain A) in PDB entry 2X1L
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 GLY 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A VAL* 2.8 24.1 + - - -
317A ASP 4.6 0.6 + - - -
318A THR 3.7 0.6 - - - -
319A PHE* 1.3 72.1 - - - +
321A LEU* 1.3 66.3 + - - -
323A GLN* 3.3 15.0 + - - +
324A VAL* 3.2 23.4 + - - +
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Residues in contact with LEU 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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84A LYS 3.4 19.3 - - - +
85A LEU* 3.6 40.6 - - + +
86A ASN* 3.7 25.8 - - + +
316A VAL* 3.9 25.2 - - + +
320A GLY* 1.3 70.1 - - - -
322A ASP* 1.3 64.2 + - - +
324A VAL* 3.1 4.6 + - + +
325A ARG* 2.9 45.1 + - + +
471A GLU* 3.9 20.0 - - - +
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Residues in contact with ASP 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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86A ASN* 5.8 0.2 + - - -
320A GLY 3.5 0.2 - - - -
321A LEU* 1.3 84.2 - - - +
323A GLN* 1.3 63.0 + - - +
325A ARG* 3.9 12.4 - - - -
326A TYR* 3.1 29.8 + - - +
469A MET* 3.6 29.2 - - + +
470A PRO* 3.7 17.0 - - - +
471A GLU* 3.5 13.4 + - - +
472A SER* 2.7 48.6 + - - +
509A PHE* 5.1 0.7 - - + -
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Residues in contact with GLN 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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319A PHE* 3.3 27.7 - - + +
320A GLY* 3.4 18.8 - - - +
321A LEU 3.2 0.4 + - - -
322A ASP* 1.3 82.1 + - - +
324A VAL* 1.3 59.8 + - - +
326A TYR* 4.0 2.1 - - - +
327A PHE* 3.1 28.6 + - - +
345A ILE* 5.8 0.7 - - - -
349A VAL* 3.8 32.2 - - + +
353A LEU* 3.8 21.7 - - + +
472A SER* 5.3 2.2 + - - -
508A ILE 4.7 1.4 + - - -
509A PHE* 3.8 26.6 - - - +
510A PRO* 4.1 24.0 + - - +
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Residues in contact with VAL 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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20A ILE* 5.0 7.0 - - + -
23A ALA* 6.3 0.7 - - + -
27A ILE* 4.8 5.6 - - + -
85A LEU* 5.6 1.1 - - + -
312A PRO* 5.4 2.5 - - + +
315A LEU* 3.5 43.3 - - + +
316A VAL* 3.9 15.0 - - + +
319A PHE* 4.4 9.2 - - + -
320A GLY 3.4 12.6 - - - +
321A LEU* 3.1 7.5 + - + +
323A GLN* 1.3 74.5 - - - +
325A ARG* 1.3 66.1 + - + +
327A PHE* 3.3 7.5 + - + +
328A LEU* 3.1 45.2 + - + +
345A ILE* 5.7 3.4 - - + -
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Residues in contact with ARG 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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27A ILE* 3.8 38.2 + - + +
30A ASP* 2.8 36.5 + - - +
31A ALA* 4.5 2.8 - - - +
85A LEU 2.9 20.8 + - - -
86A ASN* 3.7 4.9 + - - +
87A ILE* 4.0 6.5 - - - +
321A LEU* 2.9 33.6 + - + +
322A ASP* 3.9 20.2 - - - +
324A VAL* 1.3 77.2 - - - +
326A TYR* 1.3 60.7 + - - +
328A LEU* 3.7 1.4 + - - +
329A LEU* 3.4 28.6 + - - +
467A PRO 2.9 26.7 + - - -
468A VAL* 2.7 28.6 + - - +
470A PRO* 3.6 15.1 - - - +
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Residues in contact with TYR 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 ASP 3.1 19.0 + - - +
323A GLN 4.0 2.7 - - - +
325A ARG* 1.3 74.4 - - - +
327A PHE* 1.3 67.6 + - - +
329A LEU* 3.3 2.8 + - - +
330A ARG* 3.0 40.0 + - + +
348A ARG* 3.6 29.4 - - + -
352A ASP* 2.7 36.5 + - + +
353A LEU* 3.9 21.5 - - + -
413A LEU* 3.8 29.1 - - + +
417A TRP* 3.5 40.0 - + - -
468A VAL* 3.9 11.3 - - + +
469A MET* 4.0 13.5 - - + -
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Residues in contact with PHE 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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295A LEU* 5.9 1.6 - - + -
323A GLN 3.1 19.2 + - - +
324A VAL* 3.3 7.2 + - + +
326A TYR* 1.3 82.7 - - - +
328A LEU* 1.3 75.0 + - + +
330A ARG* 4.7 0.2 - - - -
331A GLU* 2.9 69.6 + - + +
340A TYR* 3.7 35.7 - + + -
344A ALA* 3.5 22.2 - - + -
345A ILE* 3.7 36.1 - - + +
348A ARG* 3.7 25.8 - - + -
349A VAL* 5.8 0.7 - - + -
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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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20A ILE* 3.9 20.2 - - + -
23A ALA* 4.4 0.7 - - + -
24A TYR* 3.3 51.2 + - + +
27A ILE* 3.7 30.5 - - + -
295A LEU* 3.6 28.5 - - + -
315A LEU* 6.1 0.2 - - + -
324A VAL* 3.1 28.4 + - + +
325A ARG 4.1 3.4 - - - +
327A PHE* 1.3 94.2 - - + +
329A LEU* 1.3 65.3 + - + +
331A GLU* 5.2 0.9 - - - -
332A VAL* 4.2 14.3 + - - +
340A TYR* 5.9 1.1 - - + -
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Residues in contact with LEU 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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24A TYR* 4.7 8.1 - - + +
27A ILE* 4.0 15.3 - - + +
28A ALA* 3.7 32.1 - - + +
31A ALA* 3.9 28.7 - - + -
325A ARG 3.4 16.5 + - - +
326A TYR 3.3 1.8 + - - +
327A PHE 3.2 0.4 - - - -
328A LEU* 1.3 81.9 - - + +
330A ARG* 1.3 58.2 + - - +
332A VAL 4.4 3.8 - - - +
334A PHE* 5.1 3.8 - - + +
409A MET* 4.2 20.8 - - + +
410A HIS* 3.2 30.4 + - - +
413A LEU* 3.5 14.6 - - + +
468A VAL* 4.3 18.2 - - + -
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Residues in contact with ARG 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 TYR* 3.0 45.8 + - + +
327A PHE 4.1 1.1 - - - +
329A LEU* 1.3 81.1 - - - +
331A GLU* 1.3 65.9 + - - +
332A VAL 3.4 2.4 + - - -
333A PRO* 5.6 0.2 - - - +
348A ARG* 3.6 40.7 - - - +
352A ASP* 4.2 1.8 + - - -
410A HIS* 4.2 10.4 - - - +
413A LEU* 3.8 24.7 - - + -
414A GLU* 3.2 44.1 + - - +
417A TRP* 5.8 3.6 - - - +
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Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 6.2 0.2 - - + -
298A ARG* 5.6 2.3 + - - -
327A PHE* 2.9 52.2 + - + +
328A LEU* 5.0 1.6 - - - +
330A ARG* 1.3 81.5 + - - +
332A VAL* 1.3 68.7 + - + +
333A PRO* 3.9 6.6 - - - +
339A SER 4.4 13.2 - - - +
340A TYR* 5.2 0.7 - - + -
344A ALA* 4.2 15.6 - - - +
348A ARG* 3.0 36.2 + - - +
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Residues in contact with VAL 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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24A TYR* 4.1 18.3 + - + +
295A LEU* 3.9 28.3 - - + -
328A LEU* 4.2 11.7 + - - +
329A LEU* 4.4 4.5 - - - +
330A ARG 4.5 2.5 - - - -
331A GLU* 1.3 90.7 - - + +
333A PRO* 1.3 78.5 - - + +
334A PHE* 3.1 6.2 + - - +
336A GLN 3.4 25.8 - - - +
337A ASP 4.0 3.1 - - - +
338A GLY* 3.9 22.7 - - - +
339A SER 4.6 2.0 - - - +
410A HIS* 3.9 10.1 - - - +
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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