Contacts of the helix formed by residues 320 - 332 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C VAL* 2.8 18.1 + - - -
317C ASP 4.6 0.8 + - - -
318C THR 3.6 0.8 - - - -
319C PHE* 1.3 79.7 - - - +
321C LEU* 1.3 64.5 + - - -
323C GLN* 3.4 11.7 + - - -
324C VAL* 3.2 23.6 + - - +
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 5.4 0.2 - - + -
84C LYS 3.5 17.5 - - - +
85C LEU* 3.6 30.1 - - + +
86C ASN* 3.7 22.0 - - + +
316C VAL* 3.8 32.4 + - + +
320C GLY* 1.3 71.8 - - - -
322C ASP* 1.3 63.2 + - - +
324C VAL* 3.2 4.2 + - + +
325C ARG* 2.9 46.8 + - + +
470C PRO* 6.3 0.2 - - + -
471C GLU* 3.7 23.1 - - - +
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Residues in contact with ASP 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C GLY 3.5 0.4 - - - -
321C LEU* 1.3 80.9 - - - +
323C GLN* 1.3 67.6 + - - +
325C ARG* 3.9 11.1 - - - -
326C TYR* 3.0 29.8 + - - +
469C MET* 3.5 38.7 - - + +
470C PRO* 3.6 10.7 - - - +
471C GLU* 3.6 12.5 + - - +
472C SER* 2.7 47.5 + - - +
509C PHE* 5.0 0.4 - - + -
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Residues in contact with GLN 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PHE* 3.2 31.0 + - + +
320C GLY* 3.4 14.8 - - - +
321C LEU 3.2 0.4 + - - -
322C ASP* 1.3 83.1 + - - +
324C VAL* 1.3 58.5 + - - +
326C TYR* 3.9 2.1 - - - +
327C PHE* 3.0 29.2 + - - +
345C ILE* 6.0 0.2 - - - -
349C VAL* 3.7 33.8 - - + +
353C LEU* 3.8 22.2 - - + +
472C SER* 5.3 2.4 + - - -
508C ILE 4.7 2.2 + - - -
509C PHE* 4.1 30.3 - - - +
510C PRO* 4.6 13.5 + - - +
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Residues in contact with VAL 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 5.1 5.8 - - + -
23C ALA* 6.4 0.7 - - + -
27C ILE* 4.7 5.8 - - + -
85C LEU* 5.8 0.7 - - + -
312C PRO* 5.5 2.2 - - + +
315C LEU* 3.4 42.6 - - + +
316C VAL* 3.9 15.0 - - + +
319C PHE* 4.2 10.1 - - + -
320C GLY 3.2 13.4 + - - +
321C LEU 3.2 7.7 + - - +
323C GLN* 1.3 72.5 - - - +
325C ARG* 1.3 67.1 + - + +
327C PHE* 3.3 6.6 + - + +
328C LEU* 3.1 45.3 + - + +
345C ILE* 5.7 4.3 - - + -
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Residues in contact with ARG 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 3.8 39.5 + - + +
30C ASP* 2.8 35.7 + - - +
31C ALA* 4.5 2.4 - - - +
85C LEU 2.8 28.5 + - - -
86C ASN* 3.7 5.5 + - - +
87C ILE* 4.2 6.1 - - - +
321C LEU* 2.9 35.8 + - + +
322C ASP* 3.8 18.2 - - - +
323C GLN 3.4 0.2 - - - -
324C VAL* 1.3 78.4 - - - +
326C TYR* 1.3 59.4 + - - +
328C LEU* 3.7 0.9 + - - +
329C LEU* 3.4 28.6 + - - +
467C PRO 2.9 26.1 + - - -
468C VAL* 2.7 27.6 + - - +
470C PRO* 3.7 14.3 - - - +
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Residues in contact with TYR 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C ASP 3.0 17.7 + - - +
323C GLN 3.9 3.1 - - - +
325C ARG* 1.3 74.5 - - - +
327C PHE* 1.3 67.6 + - - +
329C LEU* 3.3 2.8 + - - +
330C ARG* 3.0 40.2 + - + +
348C ARG* 3.7 28.7 - - + -
349C VAL* 6.3 0.4 - - + -
352C ASP* 2.7 37.1 + - + +
353C LEU* 3.8 25.6 - - + -
413C LEU* 3.9 28.0 - - + -
417C TRP* 3.6 37.3 - + - -
468C VAL* 3.9 10.3 - - + +
469C MET* 3.9 14.8 - - + -
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Residues in contact with PHE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 5.9 2.7 - - + -
323C GLN 3.0 18.4 + - - +
324C VAL* 3.3 6.9 + - + +
326C TYR* 1.3 82.2 - - - +
328C LEU* 1.3 76.5 + - + +
331C GLU* 2.9 67.0 + - + +
340C TYR* 3.7 33.2 - + + -
344C ALA* 3.4 24.5 - - + -
345C ILE* 3.7 37.5 - - + +
348C ARG* 3.7 26.2 - - + -
349C VAL* 5.5 1.8 - - + -
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Residues in contact with LEU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ILE* 4.0 22.4 - - + -
23C ALA* 4.6 1.1 - - + -
24C TYR* 3.2 45.7 + - + +
27C ILE* 3.7 30.7 - - + -
295C LEU* 3.6 28.6 - - + +
315C LEU* 6.1 0.2 - - + -
324C VAL* 3.1 29.5 + - + +
325C ARG 4.1 4.0 - - - +
327C PHE* 1.3 94.9 - - + +
329C LEU* 1.3 63.0 + - + +
331C GLU* 5.3 0.7 - - - -
332C VAL* 4.4 12.0 + - - +
340C TYR* 5.9 1.1 - - + -
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Residues in contact with LEU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR* 4.7 8.1 - - + -
27C ILE* 4.2 13.5 - - + -
28C ALA* 3.7 32.5 - - + +
31C ALA* 3.8 28.5 - - + -
325C ARG 3.4 17.9 + - - +
326C TYR 3.3 1.4 + - - -
327C PHE 3.2 0.6 - - - -
328C LEU* 1.3 81.2 - - - +
330C ARG* 1.3 58.4 + - - +
332C VAL 4.2 3.6 - - - +
334C PHE* 5.1 2.8 - - + +
409C MET* 4.1 21.4 - - + +
410C HIS* 3.2 30.1 + - - +
413C LEU* 3.7 14.8 - - + +
468C VAL* 4.2 20.0 - - + -
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Residues in contact with ARG 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C TYR* 3.0 45.4 + - + +
327C PHE 4.2 0.7 - - - +
329C LEU* 1.3 78.5 - - - +
331C GLU* 1.3 66.6 + - - +
332C VAL 3.4 3.2 + - - -
333C PRO* 5.0 0.5 - - - +
348C ARG* 3.7 40.1 - - - +
352C ASP* 4.3 1.8 + - - -
410C HIS* 4.1 9.9 - - - +
413C LEU* 3.8 24.7 - - + -
414C GLU* 3.4 43.8 + - - +
417C TRP* 5.9 2.6 - - - +
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Residues in contact with GLU 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 6.3 0.7 - - + -
298C ARG* 5.9 0.3 + - - -
327C PHE* 2.9 52.3 + - + +
328C LEU* 5.2 0.9 - - - +
330C ARG* 1.3 79.0 + - - +
332C VAL* 1.3 69.8 + - + +
333C PRO* 3.9 7.0 - - - +
339C SER 4.6 12.2 - - - +
344C ALA* 4.4 13.0 - - - +
348C ARG* 3.1 39.8 + - - +
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Residues in contact with VAL 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 4.2 18.6 + - + +
295C LEU* 3.8 20.9 - - + -
328C LEU 4.4 9.0 + - - +
329C LEU* 4.2 5.2 - - - +
330C ARG 4.5 2.7 - - - -
331C GLU* 1.3 90.7 - - + +
333C PRO* 1.3 76.1 - - + +
334C PHE* 3.2 5.2 + - - +
336C GLN 3.4 26.5 - - - +
337C ASP 4.0 3.8 - - - +
338C GLY* 3.7 31.2 - - - +
339C SER 4.5 2.9 - - - +
410C HIS* 4.0 8.9 - - - +
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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