Contacts of the helix formed by residues 345 - 361 (chain B) in PDB entry 1LL9
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 PRO 345 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLN* 3.6 17.9 - - - +
343B ASN 4.8 0.7 - - - +
344B TYR* 1.3 90.9 - - + +
346B ASN* 1.3 65.0 + - - +
347B PRO* 3.3 11.2 - - + -
348B ALA* 3.3 19.5 + - + +
349B ARG* 3.4 10.4 + - - +
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Residues in contact with ASN 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B SER* 3.2 28.2 + - - +
289B ASN* 3.1 33.5 + - - +
316B THR* 3.8 22.1 + - + -
317B GLY 5.0 0.3 + - - -
318B ALA* 5.6 0.2 - - - +
344B TYR 3.4 0.6 + - - -
345B PRO* 1.3 71.3 - - - +
347B PRO* 1.3 68.5 - - + +
349B ARG* 2.9 51.2 + - - +
350B VAL* 3.0 15.8 + - - +
964B AXL 4.6 7.6 + - - +
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Residues in contact with PRO 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ILE* 3.8 32.3 - - + +
285B ASN* 5.6 1.3 - - - +
287B SER* 3.4 9.4 - - - +
288B ASP* 4.0 29.6 - - + +
345B PRO* 3.4 12.3 - - + -
346B ASN* 1.3 93.9 - - + +
348B ALA* 1.3 54.9 + - - +
350B VAL* 3.8 0.8 - - + +
351B ASP* 2.8 33.4 + - - +
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.0 19.5 - - + +
23B GLN* 3.9 22.4 - - - +
344B TYR* 4.1 6.3 - - + -
345B PRO* 3.3 15.7 + - + +
346B ASN 3.2 0.6 - - - -
347B PRO* 1.3 80.5 - - - +
349B ARG* 1.3 61.1 + - - +
351B ASP* 4.0 5.7 - - - +
352B ALA* 3.2 24.8 + - - +
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Residues in contact with ARG 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B THR* 4.4 2.2 - - + -
317B GLY 2.7 30.2 + - - +
318B ALA* 3.7 4.8 - - - +
323B GLY* 3.6 14.4 - - - -
324B SER 3.0 20.6 + - - +
325B TYR* 4.2 19.1 - - + -
338B MET* 3.7 14.0 - - + +
343B ASN* 2.7 33.9 - - - +
344B TYR* 2.8 49.6 + - + +
345B PRO 3.4 6.3 + - - +
346B ASN* 2.9 33.5 + - - +
348B ALA* 1.3 75.4 - - - +
350B VAL* 1.3 61.2 + - + +
352B ALA* 3.4 4.2 + - - +
353B ALA* 2.9 28.1 + - - +
964B AXL 5.0 0.6 + - - -
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE* 3.7 43.7 - - + +
284B ILE* 3.9 8.1 - - + -
287B SER* 3.7 24.7 - - - +
312B TRP* 5.1 0.7 - - + -
314B HIS* 5.2 2.0 - - + +
316B THR* 4.5 2.9 - - + -
325B TYR* 3.8 38.8 - - + +
346B ASN 3.0 14.6 + - - +
347B PRO 4.0 2.2 - - - +
349B ARG* 1.3 73.0 - - + +
351B ASP* 1.3 62.2 + - - +
353B ALA* 3.1 1.2 + - - +
354B TRP* 2.7 29.6 + - - +
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Residues in contact with ASP 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B THR* 6.0 0.2 - - - +
284B ILE* 3.8 29.2 - - + +
347B PRO 2.8 20.1 + - - +
348B ALA* 4.0 7.0 - - - +
350B VAL* 1.3 76.6 - - - +
352B ALA* 1.3 65.7 + - - +
354B TRP* 3.3 2.6 + - - +
355B GLN* 3.0 42.8 + - - +
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B THR* 3.6 24.0 - - + +
16B ILE* 4.1 7.2 - - + -
19B LEU* 4.2 9.2 - - + -
338B MET* 4.0 15.7 - - + -
348B ALA 3.2 16.9 + - - +
349B ARG 3.6 3.4 - - - +
351B ASP* 1.3 84.2 - - - +
353B ALA* 1.3 62.9 + - - +
355B GLN* 3.3 3.5 + - - +
356B ILE* 3.2 29.1 + - - +
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Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TRP* 4.4 7.0 - - + -
325B TYR* 3.3 36.8 - - + -
336B ILE* 4.0 19.3 - - + -
338B MET* 4.0 11.6 - - - -
349B ARG 2.9 12.0 + - - +
350B VAL 3.6 2.2 - - - +
352B ALA* 1.3 76.4 - - - +
354B TRP* 1.3 63.3 + - - +
356B ILE* 3.3 2.9 + - - +
357B LEU* 3.0 28.1 + - - +
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Residues in contact with TRP 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B TRP* 3.4 31.9 - + - -
277B PRO* 6.2 1.3 - - + -
278B VAL* 3.5 29.6 - - + -
280B PRO* 3.2 36.8 - - + +
283B ILE* 4.4 10.8 - - + -
284B ILE* 4.8 7.0 - - + -
312B TRP* 3.9 22.8 - + + -
350B VAL 2.7 21.2 + - - +
351B ASP* 3.5 7.0 - - - +
353B ALA* 1.3 73.4 - - - +
355B GLN* 1.3 85.2 + - - +
358B ASN* 2.9 68.8 + - + +
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Residues in contact with GLN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.9 10.4 - - + +
15B THR* 4.1 20.9 - - + +
351B ASP* 3.0 35.4 + - - +
352B ALA 3.6 7.0 - - - +
354B TRP* 1.3 96.7 - - - +
356B ILE* 1.3 62.4 + - - +
358B ASN* 4.4 1.4 - - - +
359B ALA* 3.3 24.6 + - - +
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Residues in contact with ILE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.8 24.0 - - + +
12B VAL* 4.2 14.8 - - + -
15B THR* 4.0 16.4 - - - +
16B ILE* 3.8 29.8 - - + -
30B VAL* 5.4 0.2 - - + -
32B VAL* 4.3 11.2 - - + -
336B ILE* 3.6 31.2 - - + -
352B ALA 3.2 13.2 + - - +
353B ALA 3.7 5.8 - - - +
355B GLN* 1.3 74.5 - - - +
357B LEU* 1.3 70.6 + - + +
359B ALA* 3.2 4.3 + - - +
360B LEU* 3.2 34.6 + - + +
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL* 4.9 2.9 - - + -
276B TRP* 5.4 1.1 - - - -
312B TRP* 3.9 32.1 - - + -
327B ALA 4.0 16.2 - - - +
328B PHE* 4.7 1.8 - - - -
329B ILE* 4.7 7.6 - - + -
334B LEU* 3.4 35.0 - - + +
335B GLY* 3.8 23.8 - - - +
336B ILE* 3.9 23.3 - - + -
353B ALA 3.0 16.5 + - - +
356B ILE* 1.3 84.1 - - + +
358B ASN* 1.3 58.7 + - - +
360B LEU* 3.2 1.3 + - + -
361B GLN* 2.7 32.9 + - - +
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Residues in contact with ASN 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B TRP* 4.2 11.3 - - - -
354B TRP* 2.9 63.9 + - + +
355B GLN* 4.4 2.5 - - - +
357B LEU* 1.3 79.1 - - - +
359B ALA* 1.3 62.9 + - - +
361B GLN* 3.5 18.6 + - - +
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Residues in contact with ALA 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLN* 4.2 13.7 + - + +
11B ILE* 3.8 24.0 - - + -
355B GLN 3.3 18.3 + - - +
356B ILE 3.2 5.8 + - - +
357B LEU 3.2 0.6 - - - -
358B ASN* 1.3 81.7 - - - +
360B LEU* 1.3 62.3 + - + +
361B GLN 3.8 1.2 + - - -
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLN* 3.5 43.6 - - + +
8B ILE* 3.9 23.3 - - + -
11B ILE* 4.5 7.6 - - + -
32B VAL* 3.8 28.7 - - + -
34B TYR* 3.8 22.7 + - + -
334B LEU* 3.9 23.2 - - + +
356B ILE* 3.2 26.5 + - + +
357B LEU* 3.9 1.1 - - + +
359B ALA* 1.3 80.3 - - + +
361B GLN* 1.3 66.6 + - - +
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Residues in contact with GLN 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B TRP* 4.0 20.4 - - + -
332B LYS* 3.9 32.9 + - + +
334B LEU* 3.9 10.1 - - + -
357B LEU 2.7 20.9 + - - +
358B ASN* 3.8 15.4 - - - +
359B ALA 3.4 2.6 - - - +
360B LEU* 1.3 79.4 - - - +
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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
------------------------------------------------------------
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