Contacts of the strand formed by residues 307 - 311 (chain E) in PDB entry 1NZX
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 ARG 307 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E LYS* 2.9 35.9 + - + +
273E SER 3.3 2.9 + - - +
274E PRO* 3.2 18.6 - - + +
275E ASN 2.8 29.7 + - - -
305E GLY 3.2 2.1 - - - -
306E SER* 1.3 83.2 - - - +
308E THR* 1.3 56.0 + - - +
309E PHE* 3.4 35.7 + - + -
391E ASP* 5.2 3.7 + - - +
396E ALA* 3.2 32.3 - - - +
406E GLN* 5.3 0.2 - - + -
408E LEU* 3.9 16.4 - - + -
419E ARG 3.1 24.2 + - - -
420E ALA 2.9 21.2 + - - -
422E ASN 4.4 5.7 + - - -
423E SER* 3.9 16.5 - - - -
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Residues in contact with THR 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E ASN* 3.5 17.5 + - - +
277E ILE* 4.3 5.2 - - + -
290E ALA* 4.3 8.2 + - + -
305E GLY 3.7 12.3 + - - -
307E ARG* 1.3 69.2 - - - +
309E PHE* 1.3 56.2 + - - +
310E VAL* 3.7 6.5 + - + -
318E PHE* 3.8 34.8 - - + -
405E MET* 3.7 18.9 - - + +
406E GLN 2.9 18.9 + - - -
407E ILE* 3.3 9.2 - - - +
408E LEU* 2.7 34.0 + - - +
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Residues in contact with PHE 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E PRO* 3.8 20.2 - - + -
275E ASN 2.9 9.7 + - - +
276E ILE* 4.3 4.9 - - + -
277E ILE* 2.8 34.5 + - - +
307E ARG* 3.5 48.2 - - + -
308E THR* 1.3 72.5 - - - +
310E VAL* 1.3 57.7 + - - +
391E ASP* 4.1 2.2 - - - -
408E LEU* 3.4 29.8 - - + -
410E PHE* 3.6 6.9 - + + -
416E VAL* 3.6 31.4 - - + -
419E ARG* 3.8 50.0 - - + -
420E ALA* 4.3 3.8 - - + -
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Residues in contact with VAL 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E ILE* 3.9 6.3 - - + -
308E THR* 3.9 7.0 - - + +
309E PHE* 1.3 78.3 - - - +
311E GLN* 1.3 70.1 + - - +
312E GLU 3.4 0.3 + - - -
314E ILE* 3.8 15.3 - - + -
315E TYR* 3.5 33.5 - - + -
318E PHE* 3.6 42.4 - - + -
407E ILE* 3.7 17.7 - - + -
408E LEU 2.8 11.5 + - - +
409E LYS* 3.4 7.4 - - - +
410E PHE* 3.1 22.4 + - - -
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Residues in contact with GLN 311 (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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277E ILE 3.2 8.4 + - - +
278E MET* 4.9 4.7 - - + -
279E SER* 3.5 39.0 - - - +
310E VAL* 1.3 71.1 - - - +
312E GLU* 1.3 87.4 + - - +
313E ASP* 2.8 45.6 + - - +
314E ILE* 3.0 7.6 + - + +
315E TYR 3.0 17.5 + - - -
410E PHE* 3.0 24.0 - - + -
411E LYS* 2.9 30.4 + - - +
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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