Contacts of the helix formed by residues 353 - 365 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349C PHE* 3.5 25.6 - - + -
351C GLU 3.3 8.5 - - - +
352C LYS* 1.3 90.4 - - - +
354C TRP* 1.3 67.1 + - - +
355C HIS* 3.2 24.5 - - + +
356C LEU* 3.1 32.3 + - + -
357C LEU* 3.1 10.2 + - - +
144D LYS* 6.1 2.0 - - - -
241D PRO* 3.8 23.1 - - + -
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Residues in contact with TRP 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B HIS* 4.5 6.3 - + - -
353C PRO* 1.3 72.2 - - - +
355C HIS* 1.3 93.8 + - + +
357C LEU* 3.3 14.5 + - - +
358C ARG* 3.0 55.2 + - + +
241D PRO* 4.3 14.0 - - + +
242D TRP* 2.8 66.5 + + - +
244D TYR* 3.6 43.3 - + + -
276D THR* 4.9 3.6 - - + -
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Residues in contact with HIS 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B HIS* 3.9 15.9 - + + -
296B ASP* 3.7 33.9 + - + +
349C PHE* 4.6 5.0 - + - -
353C PRO* 3.4 33.4 - - + +
354C TRP* 1.3 113.1 + + + +
356C LEU* 1.3 69.0 + - + +
358C ARG* 3.5 3.9 + - - +
359C GLN* 3.0 36.9 + - - +
240D MET* 3.5 34.0 - - - +
241D PRO* 4.2 5.6 - - + +
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Residues in contact with LEU 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ASP 3.4 20.6 - - - +
297B THR* 4.0 10.1 - - + -
345C PHE* 4.0 20.7 - - + +
348C VAL* 3.8 37.0 - - + -
349C PHE* 4.6 2.0 - - + +
352C LYS* 4.3 11.9 - - + -
353C PRO* 3.1 27.8 + - + +
355C HIS* 1.3 94.0 - - + +
357C LEU* 1.3 60.3 + - - +
359C GLN* 3.8 20.4 - - - +
360C GLU* 2.8 31.6 + - - +
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Residues in contact with LEU 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C LYS* 3.8 47.8 - - + +
353C PRO 3.1 17.5 + - - +
354C TRP* 3.5 11.9 - - - +
356C LEU* 1.3 78.0 - - - +
358C ARG* 1.3 61.0 + - - +
360C GLU* 3.4 8.0 + - - +
361C ALA* 3.0 23.4 + - - +
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Residues in contact with ARG 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C TRP* 3.0 35.9 + - - +
355C HIS* 3.7 5.6 - - - +
357C LEU* 1.3 77.9 - - - +
359C GLN* 1.3 62.0 + - + +
361C ALA* 3.2 7.8 + - - +
362C LEU* 2.9 27.6 + - + +
244D TYR* 3.0 43.0 + - - -
276D THR* 4.8 3.6 - - - +
279D GLU* 5.7 1.6 + - - -
280D ASP* 2.7 27.6 + - - -
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Residues in contact with GLN 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ARG* 4.1 20.0 - - - +
295B PHE* 3.3 31.0 - - + +
296B ASP* 2.9 51.7 + - - +
345C PHE* 3.7 15.2 - - + -
355C HIS* 3.0 31.9 + - - +
356C LEU* 3.8 9.1 - - - +
358C ARG* 1.3 79.2 - - + +
360C GLU* 1.3 63.2 + - - +
362C LEU* 3.3 11.3 + - + +
363C LEU* 3.1 19.2 + - - +
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Residues in contact with GLU 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C GLU* 3.8 27.2 - - + +
345C PHE* 3.5 32.5 - - + -
346C GLU* 5.0 0.5 - - - +
352C LYS* 2.8 36.6 + - - +
356C LEU 2.8 17.1 + - - +
357C LEU* 3.7 10.4 - - - +
359C GLN* 1.3 77.1 - - - +
361C ALA* 1.3 62.8 + - - +
363C LEU* 3.2 3.6 + - - +
364C LYS* 2.9 26.0 + - + +
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Residues in contact with ALA 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C LEU 3.0 17.9 + - - +
358C ARG* 3.2 7.4 + - - +
360C GLU* 1.3 76.4 - - - +
362C LEU* 1.3 62.3 + - - +
364C LYS* 3.2 17.8 + - - +
365C GLU* 3.1 23.8 + - - +
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Residues in contact with LEU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ARG* 6.3 0.7 - - - +
295B PHE* 4.4 19.5 - - + -
313B ARG* 4.4 25.3 - - + +
316B ASN* 6.3 0.4 - - - +
320B ARG* 3.2 33.7 - - - +
358C ARG* 2.9 14.3 + - + +
359C GLN* 3.5 12.3 - - + +
360C GLU 3.2 0.2 - - - -
361C ALA* 1.3 77.6 - - - +
363C LEU* 1.3 63.2 + - - +
365C GLU* 3.2 29.2 + - - +
366C GLU* 4.0 3.8 + - - +
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Residues in contact with LEU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B PHE* 4.2 14.1 - - + -
306B LEU* 3.9 37.7 - - + +
313B ARG* 5.2 1.1 - - - +
341C PRO* 4.9 6.7 - - + +
342C GLU* 6.0 0.4 - - - -
344C MET* 3.2 34.3 - - + -
345C PHE* 3.6 14.1 - - + -
359C GLN 3.1 10.4 + - - +
360C GLU 3.2 7.2 + - - +
362C LEU* 1.3 80.4 - - - +
364C LYS* 1.3 53.6 + - - +
366C GLU* 2.8 57.5 + - + +
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Residues in contact with LYS 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C GLU* 2.9 17.4 + - + +
361C ALA* 3.4 15.3 - - - +
362C LEU 3.2 0.4 - - - -
363C LEU* 1.3 71.0 - - - +
365C GLU* 1.3 57.3 + - + +
366C GLU* 2.9 13.2 + - - -
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Residues in contact with GLU 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B ASN* 4.7 11.3 + - - +
320B ARG* 4.0 9.7 + - - -
361C ALA* 3.1 20.6 - - - +
362C LEU* 3.4 26.8 - - - +
363C LEU 3.1 0.8 - - - -
364C LYS* 1.3 77.0 - - + +
366C GLU* 1.3 56.7 + - - +
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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