Contacts of the helix formed by residues 424 - 438 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A ARG* 6.3 0.4 - - - -
427A GLU* 6.0 2.5 - - - -
363B GLU* 3.5 11.7 + - - -
422B GLY 3.6 0.8 + - - -
423B PRO* 1.3 73.0 - - - +
425B ALA* 1.3 58.1 + - - +
426B GLY 3.3 3.1 - - - -
427B GLU* 3.3 10.2 + - - +
428B MET* 2.9 33.3 + - - +
455B LEU* 3.9 14.2 - - - +
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Residues in contact with ALA 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B GLU* 3.1 30.0 + - + -
365B ALA* 3.2 23.8 - - + +
420B ILE* 3.7 32.8 - - + +
422B GLY 3.7 5.4 - - - +
423B PRO 3.2 3.2 + - - -
424B GLY* 1.3 76.0 - - - +
426B GLY* 1.3 57.5 + - - +
428B MET* 3.6 1.5 - - - +
429B VAL 2.9 27.5 + - - -
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Residues in contact with GLY 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ARG* 4.5 7.2 - - - -
454A THR* 3.4 15.6 - - - +
357B VAL* 3.6 30.1 - - - +
363B GLU* 2.9 14.5 + - - -
365B ALA* 4.1 0.4 - - - +
425B ALA* 1.3 76.5 - - - +
427B GLU* 1.3 57.9 + - - +
429B VAL* 3.3 11.3 - - - +
430B ASN* 3.2 15.1 - - - +
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Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ARG* 2.9 29.2 + - - +
424A GLY* 6.1 1.6 - - - -
427A GLU* 5.2 14.4 - - + -
428A MET* 5.1 2.3 - - - +
431A GLU* 5.3 0.3 - - - +
454A THR* 3.3 9.4 - - - -
455A LEU* 2.7 38.5 + - + +
456A SER* 2.8 31.9 + - - -
424B GLY* 3.3 10.8 + - - +
425B ALA 3.2 0.2 - - - -
426B GLY* 1.3 74.5 - - - +
428B MET* 1.3 67.3 + - - +
430B ASN* 3.0 22.6 + - - +
431B GLU* 4.1 1.2 + - - +
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Residues in contact with MET 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLU* 5.1 2.0 - - - +
388B PHE* 3.7 16.8 - - + -
404B VAL* 4.2 5.4 - - - -
420B ILE* 3.7 30.6 - - + +
423B PRO 4.0 7.9 - - - +
424B GLY 2.9 20.5 + - - +
425B ALA 3.6 3.6 - - - +
427B GLU* 1.3 77.2 - - - +
429B VAL* 1.3 56.5 + - - +
430B ASN 3.0 0.2 - - - -
431B GLU* 2.8 32.2 + - - +
432B ALA* 3.5 4.0 + - - +
455B LEU* 3.4 43.7 - - + +
456B SER* 4.0 8.3 - - - +
459B PHE* 3.8 31.5 - - + -
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Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ALA* 4.6 0.7 - - + -
355B PRO* 3.9 12.8 - - + -
357B VAL* 4.0 12.1 - - + -
365B ALA* 3.6 13.5 - - + +
366B TRP* 3.7 39.3 - - - +
367B VAL* 4.0 8.3 - - + -
418B ALA 5.4 0.4 - - - +
420B ILE* 3.9 8.7 - - + +
425B ALA 2.9 13.6 + - - +
426B GLY 3.3 22.2 - - - +
428B MET* 1.3 75.5 - - - +
430B ASN* 1.3 67.9 + - - +
432B ALA* 3.1 7.1 + - + +
433B ALA* 2.8 25.5 + - - +
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Residues in contact with ASN 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A GLU* 3.7 14.4 - - - +
448A VAL* 4.9 0.5 - - - +
449A CYS 4.2 3.4 + - - -
450A HIS* 3.5 26.7 + - + +
451A ALA* 3.1 32.3 - - - +
454A THR* 3.4 6.1 + - - +
456A SER* 2.6 23.8 + - - +
355B PRO* 4.3 3.6 - - - +
426B GLY 3.2 19.6 - - - +
427B GLU 3.3 8.6 - - - +
428B MET 3.0 1.4 + - - -
429B VAL* 1.3 81.2 - - - +
431B GLU* 1.3 64.7 + - - +
433B ALA* 3.7 4.6 - - - +
434B LEU* 3.3 20.4 + - - +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLU 5.3 0.3 - - - +
430A ASN* 3.6 24.2 - - - +
431A GLU* 3.8 28.6 + - + +
434A LEU* 3.5 23.9 - - + +
427B GLU 4.1 1.2 + - - +
428B MET* 2.8 16.6 + - - +
430B ASN* 1.3 77.8 - - - +
432B ALA* 1.3 61.7 + - - +
434B LEU* 3.4 1.4 + - - +
435B ALA* 3.2 16.8 + - - +
445B ILE* 4.2 3.8 - - - +
450B HIS* 2.9 35.6 + - - -
456B SER* 3.9 8.0 - - - -
459B PHE* 3.4 24.6 - - + +
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Residues in contact with ALA 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B VAL* 3.6 18.8 - - + -
415B VAL* 5.9 1.3 - - + +
418B ALA* 3.6 20.9 - - + -
420B ILE* 5.6 0.9 - - + -
428B MET 3.5 2.0 + - - +
429B VAL* 3.1 16.7 + - + +
431B GLU* 1.3 77.8 - - - +
433B ALA* 1.3 59.7 + - - +
435B ALA* 3.3 5.2 + - - +
436B LEU* 2.9 33.4 + - + +
459B PHE* 3.8 19.4 - - + -
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A VAL* 3.8 10.6 - - + +
449A CYS 3.6 23.8 - - - +
353B CYS* 4.2 13.9 - - - +
355B PRO* 4.9 3.4 - - + -
367B VAL* 4.1 10.9 - - + +
429B VAL 2.8 14.6 + - - +
430B ASN* 3.9 9.0 - - - +
431B GLU 3.4 0.2 - - - -
432B ALA* 1.3 75.4 - - - +
434B LEU* 1.3 62.9 + - - +
436B LEU* 3.4 7.7 + - - +
437B GLU* 3.0 26.2 + - - +
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A GLU* 3.6 42.6 - - + +
434A LEU* 4.3 9.4 - - + -
435A ALA* 3.9 20.9 - - + +
444A ASP 5.5 0.2 - - - +
445A ILE* 4.8 13.2 - - + -
448A VAL* 3.7 27.5 - - + +
459A PHE* 5.4 0.2 - - + -
430B ASN 3.3 11.3 + - - +
431B GLU 3.6 9.2 - - - +
432B ALA 3.2 0.6 - - - -
433B ALA* 1.3 79.5 - - - +
435B ALA* 1.3 61.8 + - - +
437B GLU* 3.3 10.0 + - - +
438B TYR* 3.3 39.8 + - + +
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A LEU* 4.0 11.8 - - + +
415B VAL* 5.3 3.1 - - + -
431B GLU 3.2 10.2 + - - +
432B ALA* 3.3 9.8 + - - +
434B LEU* 1.3 75.6 - - - +
436B LEU* 1.3 71.0 + - + +
438B TYR* 3.2 8.2 + - - -
440B ALA* 3.1 39.2 + - + +
445B ILE* 3.7 29.8 - - + -
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ASN* 4.2 22.0 - - - +
353B CYS* 4.4 16.8 - - + -
367B VAL* 4.4 13.2 - - + -
368B GLY* 3.9 29.2 - - - +
414B ARG* 4.7 5.4 + - - -
415B VAL* 3.2 46.4 - - + +
416B LEU 4.5 5.2 - - - +
417B GLY* 5.3 1.3 - - - -
418B ALA* 6.0 0.2 - - + -
432B ALA* 2.9 20.7 + - + +
433B ALA* 3.5 7.2 - - - +
435B ALA* 1.3 76.1 - - - +
437B GLU* 1.3 64.1 + - - +
439B GLY* 3.1 14.3 + - - +
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASP 5.5 0.9 - - - +
447A ARG 4.7 4.2 - - - +
448A VAL* 3.8 36.6 - - + +
449A CYS* 4.1 6.2 + - - +
350B ASP* 5.4 3.5 - - - +
353B CYS* 3.8 30.5 - - - +
433B ALA* 3.0 13.8 + - - +
434B LEU 3.4 10.1 - - - +
435B ALA 3.2 0.2 - - - -
436B LEU* 1.3 78.7 - - - +
438B TYR* 1.3 63.3 + - + +
439B GLY 3.8 0.3 + - - -
313F PRO* 3.6 22.6 - - + +
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Residues in contact with TYR 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A LEU* 5.8 1.8 - - + -
435A ALA* 5.5 1.1 - - - -
438A TYR* 3.6 41.1 + + + -
440A ALA* 3.0 27.4 - - + +
444A ASP* 2.9 41.8 + - + +
448A VAL* 6.1 0.4 - - + -
434B LEU* 3.3 44.0 + - + +
435B ALA* 3.2 8.8 + - - +
437B GLU* 1.3 82.4 - - + +
439B GLY* 1.3 63.6 + - - +
440B ALA* 4.3 1.1 - - + +
305F ASN* 3.9 13.0 - - - -
309F GLN* 2.9 40.8 + - - -
313F PRO* 4.5 14.8 - - + +
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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