Contacts of the helix formed by residues 424 - 438 (chain C) in PDB entry 1ZMC
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 424 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363C GLU* 3.5 12.6 + - - -
423C PRO* 1.3 72.3 - - - +
425C ALA* 1.3 65.3 + - - +
426C GLY 3.2 3.1 - - - -
427C GLU* 3.2 10.7 + - - +
428C MET* 2.9 28.1 + - - +
455C LEU* 4.1 12.4 - - - +
393D ARG* 6.3 0.4 - - - -
427D GLU* 6.0 3.1 - - - -
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Residues in contact with ALA 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C GLU* 3.1 25.6 + - + +
364C VAL 3.9 0.2 - - - +
365C ALA* 3.2 17.1 - - - +
420C ILE* 3.6 34.7 - - + +
422C GLY 3.4 16.6 - - - +
423C PRO 3.2 3.4 + - - -
424C GLY* 1.3 76.0 - - - +
426C GLY* 1.3 62.3 + - - +
428C MET* 3.2 1.9 + - - +
429C VAL 3.1 21.3 + - - -
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Residues in contact with GLY 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C VAL* 3.7 27.3 - - - +
359C TYR* 5.3 0.4 - - - -
363C GLU* 2.9 16.2 + - - +
365C ALA* 4.0 3.1 - - - +
425C ALA* 1.3 77.5 - - - +
427C GLU* 1.3 58.5 + - - +
429C VAL* 3.2 11.3 - - - +
430C ASN* 3.0 16.6 + - - -
393D ARG* 5.2 4.5 - - - -
454D THR* 3.6 13.3 - - - +
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Residues in contact with GLU 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C GLY* 3.2 11.0 + - - +
426C GLY* 1.3 76.9 - - - +
428C MET* 1.3 66.7 + - - +
430C ASN* 3.2 20.4 + - - +
431C GLU* 4.1 1.6 + - - +
393D ARG* 3.3 29.1 + - - +
424D GLY* 6.3 1.6 - - - -
427D GLU* 5.4 13.2 - - + -
428D MET* 5.2 1.8 - - - +
431D GLU* 5.2 0.5 - - - +
454D THR* 3.4 10.1 - - - -
455D LEU* 2.7 37.9 + - + +
456D SER* 2.9 31.3 + - - -
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Residues in contact with MET 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C PHE* 3.8 13.5 - - + -
404C VAL* 4.1 7.2 - - - -
420C ILE* 3.6 30.3 - - + -
423C PRO 4.2 6.3 - - - +
424C GLY 2.9 19.2 + - - +
425C ALA 3.2 4.5 + - - +
427C GLU* 1.3 71.8 - - - +
429C VAL* 1.3 53.5 + - - +
430C ASN 2.9 4.9 - - - -
431C GLU* 2.7 37.6 + - - +
432C ALA* 3.4 3.8 + - - +
455C LEU* 3.0 48.5 - - + +
456C SER* 3.8 7.9 - - - +
459C PHE* 3.9 30.2 - - + -
427D GLU* 5.0 2.0 - - - +
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Residues in contact with VAL 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C PRO* 3.9 11.0 - - + -
357C VAL* 4.1 11.2 - - + -
365C ALA* 3.5 21.3 - - + +
366C TRP* 3.6 40.8 - - - +
367C VAL* 3.9 10.8 - - + -
418C ALA* 5.2 0.9 - - + +
420C ILE* 3.8 8.5 - - + +
425C ALA 3.1 4.8 + - - -
426C GLY 3.2 22.0 - - - +
428C MET* 1.3 74.7 - - - +
430C ASN* 1.3 67.0 + - - +
431C GLU 3.2 0.2 - - - -
432C ALA* 3.3 6.9 + - + -
433C ALA* 2.9 25.6 + - - +
451D ALA* 4.6 0.7 - - + -
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Residues in contact with ASN 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C PRO* 4.6 1.6 - - - +
426C GLY 3.0 26.4 + - - -
427C GLU* 3.2 16.7 + - - +
428C MET 2.9 1.4 + - - -
429C VAL* 1.3 78.3 - - - +
431C GLU* 1.3 63.9 + - - +
433C ALA* 3.7 6.3 - - - +
434C LEU* 3.2 20.6 + - - +
431D GLU* 3.8 14.0 - - - +
448D VAL* 5.0 0.7 - - - +
449D CYS 4.4 1.4 - - - +
450D HIS* 3.4 19.6 + - + -
451D ALA* 2.9 29.5 + - - +
454D THR* 3.5 8.5 + - - +
456D SER* 2.8 27.6 + - - +
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Residues in contact with GLU 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C GLU 4.1 1.2 + - - +
428C MET* 2.7 15.5 + - - +
430C ASN* 1.3 79.7 - - - +
432C ALA* 1.3 62.4 + - - +
434C LEU* 3.3 1.0 + - - +
435C ALA* 3.0 19.4 + - - +
445C ILE* 4.2 4.0 - - - +
450C HIS* 3.0 32.5 + - - -
456C SER* 4.1 6.9 - - - -
459C PHE* 3.3 26.4 - - + +
427D GLU 5.3 0.5 - - - +
430D ASN* 3.7 23.6 - - - +
431D GLU* 3.8 25.9 - - + +
434D LEU* 3.5 23.0 - - + +
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Residues in contact with ALA 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C VAL* 3.8 7.4 - - + -
415C VAL* 5.9 0.8 - - + +
418C ALA* 3.5 31.9 - - + -
420C ILE* 5.6 0.9 - - + -
428C MET 3.4 2.2 + - - +
429C VAL* 3.3 17.0 + - + +
430C ASN 3.3 0.4 - - - -
431C GLU* 1.3 80.0 - - - +
433C ALA* 1.3 56.4 + - - +
435C ALA* 3.3 4.9 + - - +
436C LEU* 3.0 32.6 + - + +
459C PHE* 3.6 21.9 - - + -
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Residues in contact with ALA 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C CYS* 4.2 14.9 - - - +
355C PRO* 4.8 4.3 - - + -
367C VAL* 4.1 10.5 - - + +
429C VAL 2.9 17.1 + - - +
430C ASN* 3.9 8.1 - - - +
431C GLU 3.2 0.2 - - - -
432C ALA* 1.3 75.0 - - - +
434C LEU* 1.3 64.7 + - - +
436C LEU* 3.6 7.0 + - - +
437C GLU* 3.3 26.9 + - - +
448D VAL* 4.0 5.8 - - + -
449D CYS 3.6 23.3 - - - +
450D HIS* 6.4 0.2 - - + -
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Residues in contact with LEU 434 (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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430C ASN 3.2 14.1 + - - +
431C GLU 3.6 8.1 - - - +
432C ALA 3.2 0.4 - - - -
433C ALA* 1.3 76.0 - - - +
435C ALA* 1.3 64.8 + - - +
437C GLU* 3.2 17.3 + - - +
438C TYR* 3.6 32.3 - - + +
431D GLU* 3.7 40.6 - - + +
434D LEU* 4.3 9.0 - - + -
435D ALA* 3.9 25.4 - - + +
445D ILE* 4.9 13.5 - - + -
448D VAL* 3.6 30.9 - - + +
459D PHE* 5.4 0.4 - - + -
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Residues in contact with ALA 435 (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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415C VAL* 5.2 5.4 - - + -
431C GLU 3.0 12.8 + - - +
432C ALA* 3.4 10.8 - - - +
434C LEU* 1.3 77.5 - - - +
436C LEU* 1.3 63.0 + - + +
438C TYR* 3.1 9.2 + - - -
440C ALA* 3.0 40.3 + - + +
445C ILE* 3.7 29.4 - - + -
434D LEU* 3.8 11.1 - - + +
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Residues in contact with LEU 436 (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 ASN* 4.1 11.4 - - - +
353C CYS* 4.5 18.3 - - + -
367C VAL* 3.5 42.2 - - + -
368C GLY* 3.8 16.2 - - - +
414C ARG* 5.0 3.5 + - - -
415C VAL* 3.2 45.5 - - + +
416C LEU 4.6 6.3 - - - +
417C GLY* 5.2 1.1 - - - -
418C ALA* 5.8 1.1 - - + -
432C ALA 3.0 11.4 + - - +
433C ALA* 3.7 5.4 - - - +
435C ALA* 1.3 79.1 - - - +
437C GLU* 1.3 57.7 + - - +
439C GLY* 3.0 19.2 + - - +
440C ALA 4.9 1.6 - - - +
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Residues in contact with GLU 437 (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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350C ASP* 6.1 0.7 - - - +
353C CYS* 3.7 28.6 - - + +
433C ALA 3.3 11.2 + - - +
434C LEU 3.2 9.5 + - - +
436C LEU* 1.3 78.4 - - - +
438C TYR* 1.3 67.5 + - + +
439C GLY 3.8 0.2 + - - -
447D ARG 4.4 3.9 - - - +
448D VAL* 3.3 43.0 - - + +
449D CYS* 4.0 7.3 + - - +
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Residues in contact with TYR 438 (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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434C LEU* 3.6 44.0 + - + +
435C ALA* 3.1 9.3 + - - +
437C GLU* 1.3 82.6 - - + +
439C GLY* 1.3 62.3 + - - +
440C ALA* 4.5 0.7 - - + -
434D LEU* 6.0 2.2 - - + -
435D ALA* 5.5 0.7 - - - -
438D TYR* 3.5 57.4 + + + -
440D ALA* 3.2 20.2 - - + +
444D ASP* 3.1 43.5 + - + +
448D VAL* 6.1 0.4 - - + -
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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