Contacts of the strand formed by residues 363 - 368 (chain B) in PDB entry 1ZMD
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ARG* 2.6 34.7 + - - -
357B VAL* 5.1 0.7 - - + -
358B ILE 3.3 14.1 - - - +
359B TYR* 4.2 9.4 - - - +
360B THR 3.2 15.7 - - - +
361B HIS* 5.2 4.2 + - - +
362B PRO* 1.3 76.6 - - - +
364B VAL* 1.3 64.3 + - - +
421B LEU* 3.7 0.7 - - - +
422B GLY 3.0 36.2 + - - +
423B PRO* 5.2 0.8 - - + +
424B GLY* 3.6 10.0 - - - +
425B ALA* 3.2 14.5 + - + -
426B GLY* 2.9 28.0 + - - +
427B GLU 4.7 0.2 + - - -
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Residues in contact with VAL 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ILE* 4.2 6.1 - - + -
222B ILE* 3.7 26.2 - - + -
226B PHE* 3.4 47.3 - - + -
357B VAL* 3.3 1.9 - - - +
358B ILE* 2.7 43.2 + - + +
362B PRO 4.2 0.2 - - - +
363B GLU* 1.3 80.5 - - - +
365B ALA* 1.3 66.9 + - - +
366B TRP* 4.0 19.3 - - + -
420B ILE 3.2 11.7 - - - +
421B LEU* 3.7 5.8 - - + -
425B ALA* 4.0 1.1 - - - -
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Residues in contact with ALA 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B SER 3.2 13.5 - - - +
357B VAL* 4.0 5.4 - - + -
364B VAL* 1.3 78.4 - - - +
366B TRP* 1.3 67.4 + - - +
419B HIS* 3.6 0.2 - - - -
420B ILE* 2.8 37.1 + - + +
425B ALA* 3.3 34.3 - - + +
429B VAL* 3.7 15.7 - - + -
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Residues in contact with TRP 366 (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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188B VAL* 5.6 2.5 - - + -
214B GLY 4.1 11.0 - - - -
216B VAL 4.0 10.8 - - - -
217B GLY* 3.3 20.2 + - - -
218B ILE* 3.7 52.5 - - + -
222B ILE* 5.7 1.1 - - + -
354B VAL 4.5 0.3 - - - +
355B PRO* 3.3 3.8 - - - +
356B SER* 2.9 63.9 + - - -
358B ILE* 4.0 16.4 - - + -
364B VAL* 4.0 15.5 - - + -
365B ALA* 1.3 85.0 - - - +
367B VAL* 1.3 65.9 + - - +
368B GLY 4.7 7.4 - - - -
418B ALA 3.1 13.7 - - - +
419B HIS* 3.3 25.6 - + + +
429B VAL* 3.7 7.3 - - - +
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ASN 3.9 2.5 - - - +
353B CYS* 3.6 35.4 - - - +
354B VAL 3.9 3.1 - - - -
355B PRO* 3.9 19.1 - - + -
366B TRP* 1.3 80.8 - - - +
368B GLY* 1.3 66.1 + - - +
417B GLY* 3.5 0.3 - - - -
418B ALA* 2.9 34.2 + - + +
419B HIS* 4.8 1.4 + - - -
429B VAL* 4.0 3.1 - - + -
432B ALA* 3.8 29.8 - - + -
433B ALA* 4.1 11.7 - - - +
436B LEU* 3.9 15.0 - - + +
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Residues in contact with GLY 368 (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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217B GLY 5.7 0.7 - - - +
352B ASN* 3.2 38.7 + - - +
354B VAL 5.3 0.4 + - - -
366B TRP* 4.7 9.4 - - - -
367B VAL* 1.3 76.4 - - - +
369B LYS* 1.3 59.7 + - - +
373B GLN* 3.9 6.4 + - - +
416B LEU 3.5 9.2 - - - -
419B HIS* 5.0 0.4 - - - -
436B LEU* 3.7 9.4 - - - -
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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
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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