Contacts of the strand formed by residues 311 - 321 (chain E) in PDB entry 4ZXB
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 VAL 311 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E PRO* 6.4 1.3 - - + -
310E LYS* 1.3 75.7 - - - +
312E CYS* 1.3 69.3 + - - +
313E HIS* 4.0 7.1 + - + +
335E VAL* 3.5 37.9 - - + +
337E ASN* 4.5 15.3 - - + +
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Residues in contact with CYS 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E LYS* 4.0 18.8 - - - -
311E VAL* 1.3 77.3 - - - +
313E HIS* 1.3 61.5 + - - +
314E LEU* 3.7 7.6 + - + +
329E GLU 5.7 0.4 - - - -
330E LEU* 4.6 10.8 - - + -
333E CYS* 2.0 51.8 - - + -
335E VAL 2.9 10.5 + - - +
336E ILE* 3.7 4.6 - - + -
337E ASN 2.9 23.9 + - - -
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Residues in contact with HIS 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E VAL* 4.0 7.9 + - + +
312E CYS* 1.3 71.3 - - - +
314E LEU* 1.3 75.6 + - - +
315E LEU* 3.8 5.5 + - - +
317E GLY* 6.1 0.7 - - - -
337E ASN* 3.3 44.4 + - + +
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Residues in contact with LEU 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E CYS* 4.4 8.3 - - + +
313E HIS* 1.3 84.9 - - - +
315E LEU* 1.3 60.6 + - - +
316E GLU 3.4 0.7 + - - -
317E GLY* 3.0 19.4 + - - -
318E GLU 4.1 14.4 - - - +
319E LYS* 3.8 24.7 - - + +
330E LEU* 4.0 27.1 - - + -
336E ILE* 3.6 26.0 - - + -
337E ASN 3.0 17.9 + - - +
338E GLY* 4.2 0.2 - - - -
339E SER 3.4 31.6 - - - +
340E LEU* 3.9 4.0 - - + -
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Residues in contact with LEU 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E HIS 3.8 5.3 + - - +
314E LEU* 1.3 70.6 - - - +
316E GLU* 1.3 69.7 + - + +
317E GLY 3.2 0.2 + - - -
318E GLU 3.1 19.8 + - - +
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Residues in contact with GLU 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E LEU 3.4 1.0 + - - -
315E LEU* 1.3 76.3 - - + +
317E GLY* 1.3 54.7 + - - +
318E GLU* 3.0 18.0 + - + +
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Residues in contact with GLY 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E HIS* 6.1 0.7 - - - -
314E LEU* 3.0 19.7 + - - -
316E GLU* 1.3 73.8 - - - +
318E GLU* 1.3 57.2 + - - +
337E ASN 5.0 0.4 - - - -
338E GLY* 3.2 11.5 - - - -
339E SER* 2.8 32.7 + - - -
392E THR* 6.0 0.5 - - - +
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Residues in contact with GLU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E LEU* 4.1 5.1 - - - +
315E LEU 3.1 15.7 + - - +
316E GLU* 3.0 11.5 + - + +
317E GLY* 1.3 81.9 - - - +
319E LYS* 1.3 64.2 + - - +
320E THR* 5.9 0.7 - - - +
339E SER* 3.3 12.6 - - - +
341E ILE* 4.2 15.8 - - + +
367E TYR* 3.1 29.6 + - + +
392E THR* 6.0 2.0 - - + +
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Residues in contact with LYS 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E LEU* 3.8 22.2 - - + -
318E GLU* 1.3 77.1 - - - +
320E THR* 1.3 70.7 + - - +
321E ILE* 4.0 4.7 + - + -
326E SER* 3.6 30.6 + - - -
329E GLU* 2.9 38.3 + - - -
330E LEU* 4.2 26.0 - - + -
339E SER 3.1 7.1 + - - -
340E LEU* 3.5 11.3 - - + +
341E ILE* 2.9 24.5 + - - +
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Residues in contact with THR 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E GLU* 5.9 1.0 - - - +
319E LYS* 1.3 83.2 + - - +
321E ILE* 1.3 63.5 + - - +
322E ASP* 3.8 20.2 + - + +
326E SER* 4.2 8.5 - - - -
341E ILE* 3.2 31.8 - - + +
343E ASN* 4.3 21.8 - - + +
371E ARG* 4.7 7.5 + - - +
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Residues in contact with ILE 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E LYS* 4.7 5.8 - - + -
320E THR* 1.3 73.0 - - - +
322E ASP* 1.3 60.4 + - - +
323E SER 3.7 12.6 - - - +
326E SER* 3.5 16.2 - - - +
327E ALA* 3.8 20.0 - - + +
330E LEU* 3.8 29.4 - - + -
340E LEU* 3.9 25.4 - - + -
341E ILE 2.7 11.0 + - - +
342E ILE* 3.6 16.1 - - + -
343E ASN 2.8 26.4 + - - -
344E ILE* 3.4 19.8 - - + +
358E LEU* 4.5 12.8 - - + -
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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