Contacts of the helix formed by residues 353 - 367 (chain A) in PDB entry 1UMD
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 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A PHE* 3.7 24.5 - - + -
351A GLU 3.3 8.1 - - - +
352A LYS* 1.3 88.1 - - - +
354A TRP* 1.3 68.2 + - - +
355A HIS* 3.3 23.3 - - + +
356A LEU* 3.1 24.9 + - + -
357A LEU* 3.1 20.3 + - - +
144B LYS* 6.0 2.7 - - - -
241B PRO* 3.9 23.3 - - + -
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Residues in contact with TRP 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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353A PRO* 1.3 74.8 - - - +
355A HIS* 1.3 91.8 + - + +
357A LEU* 3.2 14.0 + - - +
358A ARG* 3.0 55.9 + - + +
241B PRO* 4.2 14.9 - - + +
242B TRP* 2.8 65.6 + + - +
244B TYR* 3.6 44.0 - + + -
276B THR* 5.0 3.4 - - + -
266D HIS* 4.5 6.3 - + - -
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Residues in contact with HIS 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PHE* 4.6 6.5 - + - -
353A PRO* 3.5 31.7 - - + +
354A TRP* 1.3 109.4 + - + +
356A LEU* 1.3 85.1 + - + +
358A ARG* 3.5 3.8 + - - +
359A GLN* 3.0 38.3 + - - +
240B MET* 3.5 32.5 - - - +
241B PRO* 4.2 6.7 - - + +
266D HIS* 3.9 18.8 - + + -
296D ASP* 3.8 24.3 + - + +
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Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PHE* 4.0 19.4 - - + +
348A VAL* 3.8 36.8 - - + -
349A PHE* 4.4 2.2 - - + +
352A LYS* 4.2 12.8 - - + -
353A PRO* 3.1 27.4 + - + +
355A HIS* 1.3 96.7 - - + +
357A LEU* 1.3 60.7 + - - +
359A GLN* 3.7 16.3 - - - +
360A GLU* 2.8 32.2 + - - +
296D ASP 3.4 23.1 - - - +
297D THR* 4.1 7.6 - - + -
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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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352A LYS* 3.9 42.0 - - + +
353A PRO 3.1 22.2 + - - +
354A TRP* 3.5 11.0 - - - +
356A LEU* 1.3 77.2 - - - +
358A ARG* 1.3 62.0 + - - +
360A GLU* 3.3 10.9 + - - +
361A ALA* 3.1 23.4 + - - +
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Residues in contact with ARG 358 (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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354A TRP* 3.0 37.3 + - + +
355A HIS* 3.7 6.7 - - - +
357A LEU* 1.3 77.4 - - - +
359A GLN* 1.3 65.9 + - + +
361A ALA* 3.3 8.2 + - + +
362A LEU* 3.0 22.4 + - + +
244B TYR* 3.0 41.3 + - - -
276B THR* 4.9 3.8 - - - +
279B GLU* 5.6 2.0 + - - -
280B ASP* 2.9 25.6 + - - -
265D ARG* 6.2 0.2 - - - +
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Residues in contact with GLN 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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345A PHE* 3.7 13.9 - - + -
355A HIS* 3.0 31.3 + - - +
356A LEU* 3.3 12.0 + - - +
358A ARG* 1.3 80.8 - - + +
360A GLU* 1.3 62.6 + - - +
362A LEU* 3.3 11.3 + - + +
363A LEU* 3.1 18.2 + - - +
265D ARG* 4.1 18.1 - - - +
295D PHE* 3.3 31.1 - - + +
296D ASP* 2.8 53.4 + - - +
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Residues in contact with GLU 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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342A GLU* 3.8 18.3 - - + +
345A PHE* 3.6 30.5 - - + -
346A GLU* 5.1 0.5 - - - +
352A LYS* 2.8 35.0 + - - +
356A LEU 2.8 16.3 + - - +
357A LEU* 3.7 11.9 - - - +
359A GLN* 1.3 74.2 - - - +
361A ALA* 1.3 66.1 + - - +
363A LEU* 3.4 2.9 + - - +
364A LYS* 3.1 55.1 + - + +
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Residues in contact with ALA 361 (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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357A LEU 3.1 13.7 + - - +
358A ARG* 3.3 11.4 + - - +
360A GLU* 1.3 77.3 - - - +
362A LEU* 1.3 64.8 + - - +
364A LYS* 3.3 21.3 + - - +
365A GLU* 3.3 15.8 + - - +
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Residues in contact with LEU 362 (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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358A ARG* 3.0 14.7 + - + +
359A GLN* 3.5 12.8 - - + +
360A GLU 3.2 0.2 - - - -
361A ALA* 1.3 76.5 - - - +
363A LEU* 1.3 63.9 + - - +
365A GLU* 3.0 51.2 + - - +
366A GLU* 3.7 3.1 + - - +
295D PHE* 4.5 8.7 - - + -
313D ARG* 4.4 36.0 - - + +
316D ASN* 6.1 2.0 - - + +
320D ARG* 4.1 24.2 - - - +
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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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341A PRO* 4.4 7.6 - - + +
342A GLU* 5.4 1.1 - - - -
344A MET* 3.3 31.0 - - + -
345A PHE* 3.6 14.8 - - + -
359A GLN 3.1 10.1 + - - +
360A GLU 3.7 7.2 - - - +
361A ALA 3.4 0.2 - - - -
362A LEU* 1.3 80.4 - - - +
364A LYS* 1.3 58.3 + - + +
366A GLU* 2.9 39.2 + - - +
367A LEU* 3.2 25.0 + - + +
295D PHE* 4.3 13.0 - - + -
306D LEU* 4.1 38.8 - - + +
313D ARG* 5.3 2.2 - - - +
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Residues in contact with LYS 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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342A GLU* 4.1 16.3 - - + +
360A GLU* 3.1 48.3 + - + +
361A ALA* 3.4 14.4 - - - +
362A LEU 3.2 0.2 - - - -
363A LEU* 1.3 77.5 - - + +
365A GLU* 1.3 61.8 + - - +
367A LEU* 3.2 37.0 + - + +
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Residues in contact with GLU 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 ALA 3.3 11.0 - - - +
362A LEU* 3.0 42.5 + - - +
364A LYS* 1.3 79.0 - - - +
366A GLU* 1.3 61.0 + - - +
367A LEU* 3.6 3.1 + - - +
316D ASN* 4.8 16.7 + - - +
320D ARG* 4.9 3.6 + - - -
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Residues in contact with GLU 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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362A LEU 3.7 2.2 + - - +
363A LEU* 2.9 25.7 + - + +
365A GLU* 1.3 79.7 - - - +
367A LEU* 1.3 63.8 + - + +
306D LEU* 4.7 10.6 - - - +
310D THR* 2.6 43.4 + - - +
312D THR* 3.8 28.7 - - + +
313D ARG* 3.8 22.3 + - - +
316D ASN* 4.9 5.8 - - - +
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Residues in contact with LEU 367 (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 PRO* 3.9 17.0 - - + -
342A GLU* 3.7 24.2 - - + +
363A LEU* 3.4 25.4 - - + +
364A LYS* 3.2 30.0 + - + +
365A GLU 4.1 3.6 - - - +
366A GLU* 1.3 85.5 - - + +
306D LEU* 4.1 31.9 - - + -
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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