Contacts of the helix formed by residues 335 - 349 (chain A) in PDB entry 1LAN
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 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A LYS* 3.6 29.5 - - - +
333A ALA 3.5 0.8 - - - -
334A GLU* 1.3 84.4 + - - +
336A ARG* 1.3 58.2 + - - +
338A ILE* 3.3 7.2 + - - +
339A LEU* 3.0 34.4 + - - +
360A LEU* 3.8 13.8 - - - +
500A LEU 4.6 1.0 + - - -
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Residues in contact with ARG 336 (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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333A ALA* 3.7 27.3 + - - +
335A GLY* 1.3 74.8 - - - +
337A LEU* 1.3 58.6 + - - +
339A LEU* 3.9 0.7 - - - +
340A ALA* 3.0 21.7 + - - +
360A LEU* 3.7 16.2 + - + +
361A THR* 4.3 11.5 - - - +
410A VAL* 5.4 1.8 - - - +
420A ASN* 3.2 32.8 + - + -
421A ILE* 4.1 10.3 - - - +
422A GLY 4.9 1.2 - - - +
428A GLY 4.8 2.0 + - - -
431A THR* 4.4 7.7 + - - -
432A ALA* 3.5 39.2 - - - +
435A PHE* 3.4 51.9 - - + +
436A LEU* 4.0 18.9 - - + +
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Residues in contact with LEU 337 (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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215A SER* 2.8 36.2 + - - +
216A PHE 4.1 0.2 + - - -
218A SER* 4.4 4.3 - - - +
219A VAL* 3.7 24.5 - - + -
312A ASN* 4.1 8.7 - - - +
318A VAL* 4.8 1.1 - - + -
326A ILE* 3.7 32.3 - - + -
328A VAL* 4.0 21.8 - - + -
331A THR 5.6 1.3 - - - +
333A ALA 3.7 12.8 - - - +
334A GLU* 3.3 9.4 - - + +
335A GLY 3.1 0.4 - - - -
336A ARG* 1.3 76.7 - - - +
338A ILE* 1.3 66.1 + - - +
340A ALA* 3.3 11.5 + - - +
341A ASP 3.8 0.9 + - - -
420A ASN* 4.0 24.9 - - + +
435A PHE* 4.4 2.9 - - + -
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Residues in contact with ILE 338 (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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216A PHE* 3.6 36.9 - - + +
219A VAL* 3.8 26.2 - - + -
250A LYS* 3.9 14.6 - - + -
251A GLY 3.8 15.3 - - - +
252A ILE* 3.9 17.7 - - + +
301A PRO* 3.8 36.5 - - + +
303A CYS* 5.3 0.4 - - - -
334A GLU 3.2 13.6 + - - +
335A GLY 3.4 10.8 - - - +
337A LEU* 1.3 74.9 - - - +
339A LEU* 1.3 66.7 + - + +
341A ASP* 3.5 6.6 + - - +
342A ALA* 3.3 18.9 + - - +
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 3.9 25.1 - - + -
249A GLY 4.3 0.9 - - - +
250A LYS* 4.0 26.0 - - + +
301A PRO* 5.2 0.7 - - + -
335A GLY 3.0 27.6 + - - +
338A ILE* 1.3 79.5 - - + +
340A ALA* 1.3 58.4 + - - +
342A ALA* 4.3 3.8 - - + -
343A LEU* 2.8 39.4 + - + +
356A ASN* 4.1 20.4 - - + +
357A ALA 4.9 0.7 - - - +
358A ALA* 3.9 24.5 - - + -
360A LEU* 4.2 6.5 - - + -
436A LEU* 3.7 27.4 - - + -
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Residues in contact with ALA 340 (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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215A SER* 4.4 6.5 - - - +
320A ALA* 4.7 3.1 - - + -
326A ILE* 4.5 2.7 - - + -
336A ARG 3.0 15.4 + - - +
337A LEU 3.5 11.9 - - - +
338A ILE 3.3 0.6 - - - -
339A LEU* 1.3 76.2 - - - +
341A ASP* 1.3 58.2 + - - +
343A LEU* 4.9 1.3 - - - -
344A CYS* 3.1 26.7 + - - +
435A PHE* 4.4 2.2 - - + -
436A LEU* 4.7 1.3 - - - +
439A PHE* 3.7 55.5 - - + +
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Residues in contact with ASP 341 (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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213A MET* 3.1 40.2 - - + +
215A SER* 3.0 17.5 + - - -
216A PHE* 2.8 30.7 + - + -
229A PHE* 5.8 0.2 - - + -
320A ALA* 3.4 7.6 - - - +
321A ARG* 2.8 31.5 + - + +
337A LEU 3.8 0.6 + - - -
338A ILE 3.5 8.1 + - - +
339A LEU 3.2 0.2 - - - -
340A ALA* 1.3 77.5 - - - +
342A ALA* 1.3 64.6 + - - +
344A CYS* 3.3 5.4 + - - +
345A TYR* 3.0 23.2 + - - +
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Residues in contact with ALA 342 (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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229A PHE* 4.0 19.6 - - + -
248A VAL* 3.5 26.9 - - + +
299A LEU* 3.9 5.6 - - + +
301A PRO* 3.8 24.2 - - + -
338A ILE 3.3 10.4 + - - +
339A LEU* 3.2 4.4 + - - +
341A ASP* 1.3 78.0 - - - +
343A LEU* 1.3 58.3 + - - +
345A TYR* 3.4 3.3 + - - +
346A ALA* 3.0 26.7 + - - +
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Residues in contact with LEU 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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248A VAL* 4.3 10.1 - - + -
339A LEU* 2.8 25.2 + - + +
340A ALA 4.0 3.1 - - - +
342A ALA* 1.3 70.4 - - - +
344A CYS* 1.3 64.2 + - - +
346A ALA* 3.3 10.9 + - - +
347A HIS* 2.8 24.6 + - - -
354A ILE* 4.0 22.4 - - + -
356A ASN* 4.1 20.2 - - + +
436A LEU* 4.1 35.0 - - + +
439A PHE* 4.0 13.2 - - + +
440A VAL* 3.9 20.2 - - + -
445A TRP* 3.9 19.1 - - - +
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Residues in contact with CYS 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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320A ALA* 6.3 0.2 - - + -
321A ARG* 3.6 40.5 + - + -
322A ASN* 3.7 33.9 - - + +
340A ALA 3.1 15.9 + - - +
341A ASP* 3.6 8.1 - - - +
343A LEU* 1.3 73.2 - - - +
345A TYR* 1.3 65.1 + - - +
347A HIS* 3.1 25.3 + - - +
348A THR* 4.1 1.7 + - - +
439A PHE* 4.2 8.0 + - + +
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Residues in contact with TYR 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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203A ARG* 4.1 3.6 + - - -
207A TRP* 3.6 22.3 - + - -
211A GLN* 3.9 18.2 - - - -
213A MET* 3.8 14.8 - - + -
229A PHE* 3.9 18.8 - + - -
231A GLU* 2.9 32.2 + - - -
299A LEU* 3.9 15.5 - - + -
321A ARG* 3.9 23.0 - - - +
341A ASP 3.0 17.2 + - - +
342A ALA* 3.6 4.5 - - - +
344A CYS* 1.3 77.2 - - - +
346A ALA* 1.3 58.7 + - - +
348A THR* 2.8 43.4 + - + -
349A PHE* 3.7 21.7 - + - -
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Residues in contact with ALA 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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246A VAL* 3.9 22.6 - - + +
248A VAL* 4.2 6.3 - - + -
299A LEU* 3.7 12.1 - - + +
342A ALA 3.0 13.8 + - - +
343A LEU* 3.4 15.5 - - - +
344A CYS 3.2 0.4 + - - -
345A TYR* 1.3 76.4 - - - +
347A HIS* 1.3 61.9 + - - +
348A THR 3.2 1.0 + - - -
349A PHE* 3.3 17.8 + - - +
351A PRO* 3.5 14.5 - - - +
354A ILE* 4.2 15.7 - - + -
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Residues in contact with HIS 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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343A LEU* 2.8 27.7 + - + -
344A CYS* 3.1 13.7 + - - +
346A ALA* 1.3 77.3 - - - +
348A THR* 1.3 57.1 + - + +
350A ASN* 2.9 32.6 + - - -
351A PRO* 3.9 6.7 - - + +
354A ILE* 4.1 13.7 - - + -
439A PHE 3.5 19.1 - - - -
440A VAL* 3.7 10.5 - - + -
441A THR* 3.1 37.9 + - + -
442A HIS* 3.5 21.6 + + + +
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Residues in contact with THR 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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321A ARG* 3.8 35.7 - - - +
344A CYS 4.4 1.3 - - - +
345A TYR* 2.8 31.4 + - + +
347A HIS* 1.3 76.9 - - + +
349A PHE* 1.3 71.5 + - - +
350A ASN* 3.2 7.9 + - - +
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Residues in contact with PHE 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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231A GLU* 3.5 28.0 - - - -
233A HIS* 4.2 6.5 - + - -
244A PRO* 3.6 26.0 - - + +
246A VAL* 4.1 9.2 - - + -
297A VAL* 4.0 22.2 - - + -
299A LEU* 4.0 11.2 - - + -
345A TYR* 3.7 35.0 - + - -
346A ALA* 3.5 18.6 - - - +
347A HIS 3.1 1.4 - - - -
348A THR* 1.3 90.4 - - - +
350A ASN* 1.3 71.3 + - - +
351A PRO 3.3 0.4 - - - -
503A MRD 3.8 27.7 + - + +
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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