Contacts of the strand formed by residues 363 - 368 (chain H) 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 GLU 363 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393G ARG* 2.8 32.3 + - - -
357H VAL* 5.4 0.4 - - + -
358H ILE 3.4 11.7 - - - +
359H TYR* 4.2 9.9 - - - +
360H THR 3.1 17.7 + - - +
361H HIS* 3.8 6.0 + - - +
362H PRO* 1.3 74.4 - - - +
364H VAL* 1.3 65.7 + - - +
421H LEU* 3.6 0.9 - - - +
422H GLY 2.8 39.1 + - - +
423H PRO* 5.3 1.1 - - + +
424H GLY* 3.5 10.8 - - - +
425H ALA* 3.1 14.6 + - + +
426H GLY* 2.8 28.4 + - - +
427H GLU 4.6 0.2 + - - -
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Residues in contact with VAL 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H ILE* 4.1 7.0 - - + -
222H ILE* 3.8 25.8 - - + -
226H PHE* 3.3 47.6 - - + -
357H VAL* 3.3 2.4 - - - +
358H ILE* 2.7 44.1 + - + +
362H PRO 4.1 0.4 - - - +
363H GLU* 1.3 81.2 - - - +
365H ALA* 1.3 66.7 + - - +
366H TRP* 3.9 19.1 - - + -
420H ILE 3.2 9.4 - - - +
421H LEU* 3.5 4.3 - - + -
425H ALA* 3.9 0.9 - - - -
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Residues in contact with ALA 365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356H SER 3.2 13.2 - - - +
357H VAL* 4.0 6.1 - - + -
364H VAL* 1.3 79.1 - - - +
366H TRP* 1.3 64.4 + - - +
418H ALA 4.1 0.2 - - - +
419H HIS* 3.7 0.2 - - - -
420H ILE* 2.7 37.8 + - + +
425H ALA* 3.3 33.2 - - + +
426H GLY 4.0 2.2 - - - +
429H VAL* 3.7 15.0 - - + -
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Residues in contact with TRP 366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H VAL* 4.7 3.6 - - + -
214H GLY 4.3 6.5 - - - -
216H VAL 4.2 9.2 + - - -
217H GLY* 3.4 20.2 + - - -
218H ILE* 3.7 51.4 - - + -
222H ILE* 5.7 1.1 - - + -
355H PRO* 3.4 2.4 - - - +
356H SER* 3.1 61.4 + - - -
358H ILE* 4.0 21.8 - - + -
364H VAL* 3.9 16.4 - - + -
365H ALA* 1.3 84.1 - - - +
367H VAL* 1.3 67.1 + - - +
368H GLY 4.7 7.4 - - - -
418H ALA 3.1 15.9 - - - +
419H HIS* 3.3 25.1 - + + +
429H VAL* 3.7 6.2 - - - +
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Residues in contact with VAL 367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352H ASN 3.9 2.0 - - - +
353H CYS* 3.6 33.4 - - - +
354H VAL 4.0 2.2 - - - -
355H PRO* 3.9 19.3 - - + -
366H TRP* 1.3 81.4 - - - +
368H GLY* 1.3 67.0 + - - +
369H LYS 4.8 0.2 - - - +
417H GLY* 3.4 1.0 - - - -
418H ALA* 3.0 30.7 + - + +
419H HIS* 4.9 0.7 + - - -
429H VAL* 3.9 5.4 - - + -
432H ALA* 3.7 31.2 - - + -
433H ALA* 4.1 12.6 - - + +
436H LEU* 4.0 15.7 - - + +
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Residues in contact with GLY 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H GLY 5.7 0.3 - - - +
352H ASN* 3.2 36.7 + - - -
354H VAL 5.2 0.8 + - - -
366H TRP* 4.7 9.0 - - - -
367H VAL* 1.3 77.7 - - - +
369H LYS* 1.3 63.4 + - - +
370H SER 4.1 0.2 + - - -
373H GLN* 4.0 5.7 + - - +
416H LEU 3.4 9.0 - - - -
436H LEU* 3.7 9.2 - - - -
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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