Contacts of the strand formed by residues 283 - 289 (chain I) in PDB entry 4ZZ7
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 LEU 283 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251I ASN* 3.5 16.6 - - + +
252I HIS 4.5 0.9 - - - +
253I ALA* 3.4 29.4 - - + +
268I LEU* 3.8 12.6 - - + -
271I ALA* 3.4 24.2 + - + -
272I ALA* 3.3 14.2 - - - +
281I MET 3.5 1.8 + - - -
282I ALA* 1.3 71.0 - - - +
284I SER* 1.3 56.2 + - - +
285I VAL 3.1 29.8 - - - +
388I LEU* 3.3 18.4 - - + +
412I THR 5.8 0.9 - - - -
413I CYS* 4.3 4.3 - - + -
439I PRO* 3.2 46.2 - - + +
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Residues in contact with SER 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249I ALA 5.2 0.3 + - - -
250I LYS* 3.5 36.1 + - - +
251I ASN 3.2 15.4 + - - -
272I ALA* 5.3 0.4 - - - +
282I ALA* 3.4 9.9 + - - -
283I LEU* 1.3 72.5 - - - +
285I VAL* 1.3 59.0 + - - +
383I ILE* 6.3 1.3 - - - -
387I VAL 4.0 15.2 - - - +
388I LEU* 3.5 5.4 - - - -
389I GLN* 2.7 34.4 + - - +
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Residues in contact with VAL 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250I LYS* 3.6 31.2 - - + -
251I ASN 3.2 3.0 + - - +
252I HIS* 3.2 40.9 - - + +
253I ALA 3.0 23.6 + - - -
283I LEU* 3.1 9.0 - - - +
284I SER* 1.3 86.2 - - - +
286I ALA* 1.3 63.3 + - - +
287I VAL* 4.1 7.0 - - + -
379I TYR* 4.1 8.5 - - + -
388I LEU* 4.4 0.9 - - - -
389I GLN* 3.2 12.1 - - + +
391I VAL* 4.0 24.2 - - + -
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Residues in contact with ALA 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253I ALA* 3.5 7.4 - - - +
255I VAL* 4.9 2.0 - - + -
268I LEU* 4.5 18.2 - - + -
285I VAL* 1.3 72.5 - - - +
287I VAL* 1.3 64.1 - - - +
288I ALA 3.4 2.7 + - - -
297I LEU* 3.9 23.3 - - + +
388I LEU* 4.2 13.6 - - + +
389I GLN 2.9 12.1 + - - +
390I VAL* 3.4 12.5 - - + +
391I VAL 3.1 21.0 + - - +
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Residues in contact with VAL 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252I HIS* 3.8 35.7 - - + -
253I ALA 2.8 11.7 + - - +
254I ILE* 3.5 5.9 - - + +
255I VAL* 3.0 26.7 + - - -
285I VAL* 4.1 6.3 - - + -
286I ALA* 1.3 69.0 - - - +
288I ALA* 1.3 60.5 + - - +
289I VAL 3.6 1.0 + - - -
391I VAL* 3.4 9.2 - - + +
393I VAL* 3.5 24.7 - - + -
399I ALA* 3.4 37.2 - - + +
402I LEU* 4.2 12.1 - - + -
403I ILE* 5.1 1.3 - - + -
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Residues in contact with ALA 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255I VAL* 4.2 7.9 - - + -
286I ALA 3.4 1.6 + - - -
287I VAL* 1.3 73.4 - - - +
289I VAL* 1.3 60.8 + - - +
290I GLY 3.5 3.2 + - - +
293I ALA* 4.1 5.8 - - + -
294I GLY* 3.5 36.3 - - - +
297I LEU* 4.3 15.3 - - + -
390I VAL* 4.7 4.5 - - + -
391I VAL 2.9 11.3 + - - +
392I ARG* 3.6 5.5 - - + -
393I VAL 3.2 23.3 + - - +
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Residues in contact with VAL 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I ILE* 4.2 7.4 - - + -
255I VAL 3.1 22.1 + - - +
256I MET* 3.5 33.0 - - + -
257I PRO* 3.8 22.1 - - + +
287I VAL 3.6 2.0 + - - -
288I ALA* 1.3 67.4 - - - +
290I GLY* 1.3 62.7 - - - +
292I ALA* 4.9 0.9 - - - +
293I ALA* 3.8 12.7 + - - +
393I VAL* 3.4 9.9 - - + +
394I ALA 3.4 20.2 - - - +
395I THR* 3.7 23.8 - - - +
396I MET* 3.9 4.3 - - + +
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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