Contacts of the helix formed by residues 342 - 357 (chain A) in PDB entry 1LC7
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 SER 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PRO* 3.7 11.2 - - - +
272A TRP* 4.5 6.5 - - - +
341A ARG* 1.3 81.0 - - - +
343A ALA* 1.3 65.5 + - - +
344A ALA* 3.6 7.7 + - - +
345A GLN* 3.1 32.8 + - - +
346A ASN* 2.8 20.7 + - - -
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Residues in contact with ALA 343 (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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272A TRP* 5.7 0.2 - - - -
276A GLU* 3.4 38.3 - - + +
279A ARG* 3.8 5.8 + - - +
342A SER* 1.3 72.5 - - - +
344A ALA* 1.3 57.9 + - - +
346A ASN* 3.2 2.3 + - - +
347A GLU* 2.8 35.1 + - + +
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Residues in contact with ALA 344 (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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342A SER* 3.2 6.8 + - - +
343A ALA* 1.3 78.9 - - - +
345A GLN* 1.3 64.1 + - + +
347A GLU* 3.2 16.5 + - - +
348A ARG* 3.2 18.6 + - - +
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Residues in contact with GLN 345 (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 LEU* 3.7 23.3 - - + +
29A PHE* 3.5 22.0 - - + -
35A PRO* 4.7 4.2 - - - +
341A ARG* 3.2 51.8 + - + +
342A SER* 3.1 25.0 + - - +
344A ALA* 1.3 77.7 - - + +
346A ASN* 1.3 67.0 + - - +
348A ARG* 3.0 17.6 + - - +
349A LEU 3.1 9.5 + - - -
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Residues in contact with ASN 346 (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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29A PHE* 3.4 16.7 - - - -
276A GLU* 2.8 26.8 + - - +
279A ARG* 4.4 2.2 - - - +
280A PHE* 3.5 35.0 - - + +
340A ILE* 3.9 2.9 - - - +
341A ARG* 2.9 42.2 + - - +
342A SER 2.8 14.1 + - - +
343A ALA 3.5 4.5 - - - +
345A GLN* 1.3 76.1 - - - +
347A GLU* 1.3 57.8 + - - +
349A LEU* 3.3 2.1 + - - +
350A LEU* 3.0 34.9 + - - +
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Residues in contact with GLU 347 (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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279A ARG* 2.3 38.6 + - - +
343A ALA* 2.8 18.0 + - + +
344A ALA* 3.4 13.0 - - - +
345A GLN 3.1 0.2 - - - -
346A ASN* 1.3 78.2 - - - +
348A ARG* 1.3 61.0 + - + +
350A LEU* 3.5 15.8 - - - +
351A ALA* 3.1 23.9 + - - +
354A ARG* 4.4 13.6 + - - -
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Residues in contact with ARG 348 (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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25A GLN 5.8 1.2 + - - -
26A LEU 5.9 0.2 - - - -
27A LEU* 3.9 36.8 - - + +
318A GLN 4.3 15.6 + - - -
319A ARG* 4.8 7.9 + - - +
320A ILE* 3.6 15.3 - - + +
344A ALA 3.2 13.1 + - - +
345A GLN* 3.0 10.3 + - - +
347A GLU* 1.3 73.5 - - + +
349A LEU* 1.3 67.0 + - - +
351A ALA* 3.4 6.2 + - - +
352A ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 349 (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 LEU* 4.9 0.6 - - - +
29A PHE* 3.6 32.8 - - + -
280A PHE* 3.5 28.9 - - + -
284A LEU* 5.0 0.4 - - + -
315A LEU* 3.6 31.2 - - + -
320A ILE* 3.8 21.5 - - + +
322A ILE* 4.0 9.2 - - + -
338A VAL* 3.8 18.6 - - + -
345A GLN 3.1 5.1 + - - -
346A ASN 3.3 7.2 + - - +
348A ARG* 1.3 77.0 - - - +
350A LEU* 1.3 61.8 + - - +
352A ALA* 3.1 3.8 + - - +
353A LEU* 2.9 35.7 + - + +
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Residues in contact with LEU 350 (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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279A ARG* 4.3 5.2 - - - +
280A PHE* 4.1 18.4 - - + -
283A ALA* 3.4 29.2 - - + +
284A LEU* 3.7 43.1 - - + +
287A LEU* 4.1 8.3 - - + -
346A ASN 3.0 18.8 + - - +
347A GLU* 3.5 24.2 - - - +
348A ARG 3.3 0.2 - - - -
349A LEU* 1.3 77.6 - - - +
351A ALA* 1.3 56.4 + - - +
353A LEU* 3.2 5.0 + - - +
354A ARG* 2.9 54.5 + - - +
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Residues in contact with ALA 351 (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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347A GLU 3.1 17.9 + - - +
348A ARG* 3.9 6.3 - - - +
349A LEU 3.3 0.2 - - - -
350A LEU* 1.3 76.8 - - - +
352A ALA* 1.3 61.1 + - - +
354A ARG* 3.5 17.9 + - - +
355A ASN* 2.8 33.2 + - - +
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Residues in contact with ALA 352 (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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315A LEU* 4.1 10.1 - - + -
318A GLN* 3.5 32.0 - - - +
320A ILE* 3.5 29.8 - - + -
348A ARG 3.1 6.2 + - - +
349A LEU 3.5 8.1 - - - +
351A ALA* 1.3 75.2 - - - +
353A LEU* 1.3 65.0 + - - +
355A ASN* 3.3 10.7 + - - +
356A VAL* 3.4 18.1 + - - +
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Residues in contact with LEU 353 (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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284A LEU* 3.6 31.4 - - + -
287A LEU* 3.7 17.5 - - + -
290A LEU* 4.7 2.5 - - + -
302A LEU* 4.6 12.1 - - + -
311A LEU* 4.0 31.6 - - + -
315A LEU* 3.7 24.5 - - + -
322A ILE* 5.7 0.4 - - + -
349A LEU* 2.9 32.4 + - + +
350A LEU* 3.7 6.3 - - - +
352A ALA* 1.3 75.4 - - - +
354A ARG* 1.3 57.2 + - - +
356A VAL* 3.1 5.4 + - - +
357A LEU* 2.8 41.0 + - + +
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Residues in contact with ARG 354 (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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283A ALA* 5.0 6.1 + - - +
287A LEU* 3.2 32.9 - - + +
347A GLU* 4.4 16.2 + - - -
350A LEU* 2.9 49.7 + - - +
351A ALA* 3.7 17.5 - - - +
353A LEU* 1.3 76.5 - - - +
355A ASN* 1.3 58.5 + - - +
357A LEU* 5.0 0.4 - - - +
358A THR* 2.7 47.8 + - - +
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Residues in contact with ASN 355 (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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318A GLN* 3.6 22.5 - - - +
351A ALA* 2.8 24.9 + - - +
352A ALA 3.3 5.8 + - - +
354A ARG* 1.3 77.1 - - - +
356A VAL* 1.3 61.5 + - + +
358A THR 4.7 5.0 - - - +
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Residues in contact with VAL 356 (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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306A ARG* 2.7 45.0 + - - +
309A ILE* 5.5 6.1 - - + -
311A LEU* 3.7 25.4 - - + -
314A ARG* 4.2 18.2 - - + -
315A LEU* 4.0 13.2 - - + -
318A GLN* 3.9 13.9 - - - +
352A ALA 3.4 14.6 - - - +
353A LEU 3.1 6.5 + - - +
354A ARG 3.1 0.4 - - - -
355A ASN* 1.3 83.0 - - + +
357A LEU* 1.3 64.7 + - + +
358A THR 3.8 1.4 - - - +
360A ILE* 5.2 1.2 - - - +
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Residues in contact with LEU 357 (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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287A LEU* 4.3 12.1 - - + -
288A PRO* 3.2 38.4 - - + +
289A LEU* 3.8 28.9 - - + +
290A LEU* 4.0 30.1 - - + -
304A CYS* 4.0 20.6 - - - -
306A ARG* 4.4 9.0 - - + +
311A LEU* 4.7 4.3 - - + -
353A LEU* 2.8 28.1 + - + +
354A ARG* 5.0 0.9 - - - -
356A VAL* 1.3 92.3 - - + +
358A THR* 1.3 61.5 + - - +
359A GLY 3.9 0.2 + - - -
360A ILE* 4.1 13.7 + - - +
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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