Contacts of the helix formed by residues 303 - 317 (chain A) in PDB entry 3L4U
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 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A TYR* 3.1 5.6 + - - +
302A GLY* 1.3 82.2 - - - +
304A LEU* 1.3 63.5 + - - +
305A ASP* 3.5 11.2 + - - +
306A ASN* 3.0 31.5 + - - +
307A MET* 3.0 20.6 + - - +
343A ASP* 3.5 30.7 - - - +
344A PHE* 3.8 7.9 - - - -
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Residues in contact with LEU 304 (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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303A THR* 1.3 71.2 - - - +
305A ASP* 1.3 54.2 + - - +
307A MET* 3.2 5.7 + - - -
308A ARG* 2.8 54.8 + - + +
343A ASP 2.9 17.6 + - - +
344A PHE* 3.7 29.8 - - + +
345A LYS 3.4 24.5 - - - +
346A GLY 3.5 6.1 - - - +
347A PHE* 3.4 27.4 - - + +
350A PHE* 3.6 36.8 - - + -
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Residues in contact with ASP 305 (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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303A THR* 3.2 11.5 + - - +
304A LEU* 1.3 80.3 - - - +
306A ASN* 1.3 59.4 + - - +
308A ARG* 3.5 22.9 + - - +
309A GLU* 3.0 27.3 + - - +
343A ASP 4.7 0.4 + - - -
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Residues in contact with ASN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A TYR* 2.8 34.7 + - + +
302A GLY* 4.8 1.0 - - - -
303A THR* 3.0 25.6 + - - +
305A ASP* 1.3 76.1 - - - +
307A MET* 1.3 66.1 + - - +
309A GLU* 3.4 17.9 + - - +
310A VAL* 3.3 27.2 + - - +
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Residues in contact with MET 307 (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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301A TYR* 3.4 47.2 - - + +
303A THR 3.0 13.3 + - - +
304A LEU* 3.6 10.8 - - + +
306A ASN* 1.3 74.1 - - - +
308A ARG* 1.3 60.1 + - - +
310A VAL* 3.2 5.2 + - - +
311A VAL* 3.0 31.1 + - + +
324A GLN* 4.2 13.9 - - - +
325A HIS 3.9 4.5 - - - +
326A ALA* 3.9 29.8 - - + -
327A ASP 5.0 0.9 - - - +
329A ASP* 5.2 1.3 - - - +
330A TYR* 5.7 0.2 - - + -
344A PHE* 4.0 23.3 - - + -
347A PHE* 4.8 2.0 - - - -
350A PHE* 3.8 32.1 - - + -
361A LEU* 5.6 0.4 - - - -
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Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 2.8 44.6 + - + +
305A ASP* 3.7 20.3 + - - +
307A MET* 1.3 71.7 - - - +
309A GLU* 1.3 57.1 + - - +
311A VAL* 3.3 1.7 + - - +
312A GLU* 2.9 40.8 + - + +
345A LYS 4.6 4.6 + - - -
346A GLY* 3.4 26.3 + - - -
349A GLU* 4.3 9.5 + - - +
350A PHE* 3.5 39.8 - - + +
353A GLU* 3.3 22.7 + - - -
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Residues in contact with GLU 309 (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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305A ASP 3.0 13.7 + - - +
306A ASN* 3.5 24.1 - - - +
307A MET 3.3 0.4 - - - -
308A ARG* 1.3 75.1 - - - +
310A VAL* 1.3 59.8 + - + +
312A GLU* 3.9 4.2 - - - +
313A ARG* 3.0 51.2 + - + +
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Residues in contact with VAL 310 (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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296A LEU* 3.8 16.6 - - + -
301A TYR* 3.8 29.6 - - + +
306A ASN* 3.4 14.1 - - + +
307A MET 3.2 7.8 + - - +
309A GLU* 1.3 75.0 - - + +
311A VAL* 1.3 66.8 + - + +
313A ARG* 3.4 28.4 + - - +
314A ASN* 2.9 32.4 + - - +
324A GLN* 5.5 0.9 - - - +
607A ASP* 5.3 3.4 - - - +
609A ASP* 3.7 25.4 - - + +
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A MET* 3.0 21.2 + - + +
308A ARG* 3.8 6.1 - - - +
310A VAL* 1.3 75.9 - - - +
312A GLU* 1.3 71.5 + - - +
314A ASN 3.3 0.3 + - - -
315A ARG* 3.0 44.6 + - - +
321A TYR* 3.3 29.7 - - + +
324A GLN* 3.7 17.5 - - + +
350A PHE* 3.9 27.1 - - + -
354A LEU* 4.3 9.4 - - + -
359A GLN* 4.1 10.5 - - - +
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Residues in contact with GLU 312 (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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308A ARG* 2.9 25.5 + - + +
309A GLU* 4.0 4.5 - - - +
311A VAL* 1.3 83.6 - - + +
313A ARG* 1.3 56.4 + - - +
315A ARG* 3.4 37.6 + - - +
316A ALA* 2.8 29.6 + - - +
353A GLU* 6.1 0.9 - - - +
357A ASN* 4.7 4.0 - - - +
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Residues in contact with ARG 313 (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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309A GLU* 3.0 48.8 + - + +
310A VAL* 3.5 24.3 - - - +
312A GLU* 1.3 76.8 - - - +
314A ASN* 1.3 60.2 + - - +
316A ALA* 3.5 7.6 + - - +
317A ALA* 3.1 22.3 + - - +
607A ASP* 3.1 25.6 + - - -
609A ASP* 2.7 38.9 + - - -
611A ALA* 3.4 29.7 - - + +
612A SER* 3.8 11.9 - - - +
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Residues in contact with ASN 314 (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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296A LEU* 3.8 10.6 - - - +
310A VAL* 2.9 29.9 + - - +
313A ARG* 1.3 76.9 - - - +
315A ARG* 1.3 63.3 + - - +
317A ALA* 3.3 6.8 + - - +
319A LEU* 3.3 39.8 + - + +
321A TYR* 3.8 22.2 - - + -
609A ASP* 2.9 30.3 + - - +
610A PRO* 3.5 12.8 - - - +
611A ALA* 3.0 29.1 + - - +
620A LEU* 5.1 0.2 - - - +
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Residues in contact with ARG 315 (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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311A VAL* 3.0 23.7 + - - +
312A GLU* 3.4 36.3 + - - +
314A ASN* 1.3 73.5 - - - +
316A ALA* 1.3 64.4 + - - +
318A GLN* 3.0 25.9 + - - +
319A LEU 5.1 2.9 - - - +
321A TYR* 4.2 5.2 - - + -
357A ASN* 3.1 50.6 + - - +
359A GLN* 3.5 32.7 + - - +
2001A NAG 5.9 1.2 + - - -
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Residues in contact with ALA 316 (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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312A GLU 2.8 22.8 + - - +
313A ARG* 3.6 9.6 - - - +
314A ASN 3.3 0.2 - - - -
315A ARG* 1.3 72.5 - - - +
317A ALA* 1.3 58.9 + - - +
318A GLN* 3.4 13.4 + - - +
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Residues in contact with ALA 317 (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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313A ARG 3.1 17.3 + - - +
314A ASN* 3.6 7.4 - - - +
315A ARG 3.1 0.6 - - - -
316A ALA* 1.3 74.4 - - - +
318A GLN* 1.3 70.2 + - - +
319A LEU* 3.4 1.9 + - + +
611A ALA* 4.4 3.1 - - + -
615A ALA* 5.9 1.1 - - + -
620A LEU* 3.6 38.8 - - + +
624A ARG* 2.7 29.6 + - - +
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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