Contacts of the helix formed by residues 352 - 367 (chain A) in PDB entry 1LD7
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 ARG 352 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ASP* 2.7 50.5 + - - +
351A ILE* 1.3 96.1 - - + +
353A LYS* 1.3 62.3 + - - +
354A GLU 3.2 3.4 - - - -
355A TYR* 3.0 12.4 + - + -
356A TRP* 3.0 30.7 + - + +
778B THR* 2.9 51.1 + - - +
779B SER* 3.5 21.4 + - - +
781B GLN* 3.1 23.6 + - + +
783B ARG* 3.1 25.5 - - - +
830B PHE* 6.0 3.8 - - - +
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Residues in contact with LYS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ALA* 3.7 30.2 - - + +
349A ASP 3.7 0.2 + - - -
350A THR* 2.9 19.0 + - - +
351A ILE 4.9 0.7 - - - +
352A ARG* 1.3 77.4 - - - +
354A GLU* 1.3 90.1 + - - +
356A TRP* 3.4 1.6 + - - +
357A ARG* 3.0 38.4 + - + +
827B HIS* 5.9 3.4 - - - -
830B PHE 4.7 0.8 + - - -
831B HIS* 3.3 46.2 + - + +
832B GLN 5.0 1.0 - - - +
833B GLN 5.9 0.2 - - - +
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Residues in contact with GLU 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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351A ILE 5.3 0.2 + - - -
352A ARG 3.2 0.8 - - - -
353A LYS* 1.3 108.3 + - - +
355A TYR* 1.3 63.0 + - - +
357A ARG* 3.5 11.2 + - - +
358A TYR* 3.1 22.9 + - - +
361A ARG* 5.1 4.7 + - - -
824B SER* 4.4 13.3 + - - -
827B HIS* 3.8 32.4 + - + +
828B TRP 3.6 23.6 - - - +
829B MET* 3.9 13.7 - - + +
830B PHE* 4.1 11.8 - - - +
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Residues in contact with TYR 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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320A GLU* 5.0 2.1 + - - -
352A ARG* 3.0 19.7 + - + +
354A GLU* 1.3 79.5 - - - +
356A TRP* 1.3 93.6 + + - +
358A TYR* 3.1 9.6 + + - +
359A ILE* 2.9 59.3 + - + +
771B LYS* 5.1 2.6 + - - +
774B LEU* 3.8 37.2 - - + -
775B GLN* 3.3 43.9 + - + +
778B THR* 4.0 28.3 - - + -
829B MET* 4.5 9.4 + - - +
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Residues in contact with TRP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ALA* 3.7 32.1 - - + -
316A VAL* 3.9 22.2 - - + -
317A ASP* 5.0 0.2 - - - -
320A GLU* 4.9 2.2 - - - -
341A CYS* 3.7 32.6 - - - +
344A LEU* 3.6 44.4 - - + +
345A ALA* 4.0 8.1 - - + -
349A ASP* 2.9 30.2 + - - -
352A ARG* 3.0 36.7 + - + +
355A TYR* 1.3 101.1 - + - +
357A ARG* 1.3 61.2 + - - +
359A ILE* 3.3 15.4 + - + +
360A GLY* 2.9 24.9 + - - -
775B GLN* 4.1 11.4 - - - -
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Residues in contact with ARG 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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341A CYS 4.9 0.6 + - - -
342A GLU* 2.4 45.1 + - - +
345A ALA* 3.7 22.2 - - - +
346A LYS* 3.9 21.0 - - - +
353A LYS* 3.0 28.9 + - + +
354A GLU* 3.8 12.8 - - - +
356A TRP* 1.3 76.3 - - - +
358A TYR* 1.3 63.8 + - - +
360A GLY* 3.2 2.6 + - - -
361A ARG* 3.0 45.3 + - + +
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Residues in contact with TYR 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLU 3.1 14.0 + - - +
355A TYR* 3.2 9.9 - + - +
357A ARG* 1.3 76.8 - - - +
359A ILE* 1.3 74.0 + - + +
361A ARG* 3.2 16.0 + - - +
362A SER* 2.8 51.4 + - - -
774B LEU* 3.7 21.5 - - + +
815B LEU* 3.7 14.0 - - + +
820B ASP* 2.4 37.8 + - - -
822B ALA* 3.6 20.9 - - + -
823B LEU* 4.0 13.0 - - + -
829B MET* 3.4 26.2 - - + -
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Residues in contact with ILE 359 (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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316A VAL* 4.2 3.6 - - + -
320A GLU* 3.5 27.6 - - - +
341A CYS* 3.6 20.0 - - - -
355A TYR* 2.9 58.1 + - + +
356A TRP* 3.3 12.8 + - + +
358A TYR* 1.3 89.1 - - + +
360A GLY* 1.3 62.0 + - - +
362A SER* 3.2 7.3 + - - +
363A LEU* 2.9 34.6 + - + +
774B LEU* 5.7 0.2 - - + -
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Residues in contact with GLY 360 (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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338A LEU* 3.5 22.6 - - - +
341A CYS* 4.1 10.7 - - - -
356A TRP 2.9 15.5 + - - -
357A ARG* 3.2 4.7 + - - -
359A ILE* 1.3 78.4 - - - +
361A ARG* 1.3 61.0 + - - +
363A LEU* 3.4 0.4 + - - -
364A GLN* 3.2 30.2 + - - +
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Residues in contact with ARG 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLU* 5.1 4.9 + - - -
357A ARG* 3.0 39.3 + - - +
358A TYR* 3.7 21.1 - - - +
360A GLY* 1.3 73.2 - - - +
362A SER* 1.3 64.4 + - - +
364A GLN* 3.3 14.2 + - - +
365A SER* 3.0 23.4 + - - -
822B ALA* 2.7 45.0 + - + +
823B LEU 4.6 1.8 + - - -
824B SER* 3.5 28.4 - - - +
829B MET* 6.0 0.6 - - - +
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Residues in contact with SER 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A TYR* 2.8 57.8 + - - -
359A ILE* 3.2 10.1 + - - -
361A ARG* 1.3 68.5 - - - +
363A LEU* 1.3 69.1 + - - +
365A SER* 2.8 23.6 + - - -
366A LYS* 3.0 32.7 + - - +
820B ASP* 4.8 1.0 + - - -
822B ALA* 3.5 6.1 - - - +
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Residues in contact with LEU 363 (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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316A VAL* 4.9 2.5 - - + -
320A GLU* 3.9 25.8 - - + -
323A LEU* 3.9 24.5 - - + -
334A LEU* 4.0 14.7 - - + +
337A ALA* 3.8 25.8 - - + -
338A LEU* 4.2 10.3 - - + -
341A CYS* 4.0 11.7 - - - -
359A ILE* 2.9 35.0 + - + +
360A GLY 3.5 3.8 - - - +
362A SER* 1.3 77.4 - - - +
364A GLN* 1.3 57.1 + - - +
366A LYS* 4.9 1.8 - - + -
367A HIS* 2.9 43.1 + - + +
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Residues in contact with GLN 364 (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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334A LEU* 5.0 7.0 - - + -
338A LEU* 4.0 29.2 - - + +
360A GLY 3.2 19.9 + - - +
361A ARG* 3.6 14.3 - - - +
362A SER 3.2 0.8 - - - -
363A LEU* 1.3 77.7 - - - +
365A SER* 1.3 64.4 + - - +
366A LYS 3.4 0.5 + - - -
367A HIS 3.8 12.9 + - - +
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Residues in contact with SER 365 (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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361A ARG 3.0 13.9 + - - -
362A SER* 2.8 22.2 + - - -
364A GLN* 1.3 76.2 - - - +
366A LYS* 1.3 65.3 + - - +
821B PRO* 3.8 33.0 - - - +
822B ALA* 4.7 2.0 - - - +
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Residues in contact with LYS 366 (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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324A GLU* 4.1 26.0 + - - +
362A SER* 3.0 32.2 + - - +
363A LEU* 5.3 0.9 - - + -
365A SER* 1.3 86.5 - - - +
367A HIS* 1.3 85.5 + - + +
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Residues in contact with HIS 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLU 4.7 2.5 - - - -
323A LEU* 3.1 52.5 + - + +
324A GLU* 3.7 21.3 + - - -
326A GLN* 5.4 0.2 - - - -
330A LYS* 3.0 38.5 - - + +
331A GLU* 4.7 8.8 - - - +
334A LEU* 3.6 27.3 - - + +
363A LEU* 2.9 25.6 + - + +
364A GLN 3.8 10.5 + - - -
365A SER 3.7 0.8 - - - -
366A LYS* 1.3 108.6 - - + +
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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