Contacts of the strand formed by residues 269 - 277 (chain A) in PDB entry 3NRN
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 GLY 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A SER* 4.8 6.7 - - - -
267A SER 4.0 0.4 + - - -
268A GLU* 1.3 75.3 - - - +
270A ILE* 1.3 66.2 + - - +
318A HIS* 5.1 4.5 - - - -
319A MSE 3.3 11.7 - - - -
320A ALA* 4.4 1.3 - - - -
321A LEU* 3.9 1.6 - - - -
350A GLN 4.5 0.2 - - - -
351A VAL* 3.6 5.2 - - - +
352A TYR* 2.7 37.5 + - - +
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A GLY* 1.3 79.8 - - - +
271A LYS* 1.3 69.5 + - - +
272A PHE* 3.4 28.7 - - + -
317A ALA 3.8 0.3 - - - +
318A HIS* 3.6 4.3 + - - -
319A MSE 2.7 70.8 + - + +
321A LEU* 3.9 13.2 - - + -
326A VAL* 4.3 10.8 - - + +
329A ALA* 3.8 13.9 - - + -
330A ILE* 3.9 22.2 - - + +
349A ALA* 4.7 2.7 - - + -
350A GLN 3.3 9.4 - - - +
351A VAL* 4.5 11.7 - - + -
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Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A SER* 3.1 33.9 + - - -
52A GLY 2.8 36.6 + - - +
54A LEU* 3.6 26.2 - - + -
270A ILE* 1.3 75.3 - - - +
272A PHE* 1.3 63.8 + - - +
273A ASN* 4.1 9.2 - - - +
316A MSE 5.0 0.7 - - + -
317A ALA 3.4 6.3 - - - +
318A HIS* 5.0 10.8 - - + -
348A LEU 3.8 1.0 - - - +
349A ALA* 3.1 7.3 - - - +
350A GLN* 2.7 58.3 + - + +
352A TYR* 3.2 24.1 + - + -
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Residues in contact with PHE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ILE* 3.4 28.3 - - + -
271A LYS* 1.3 73.2 - - - +
273A ASN* 1.3 62.0 + - - +
274A LEU* 3.8 1.1 + - - +
294A ILE* 3.4 30.3 - - + -
315A ILE* 3.4 1.7 - - - +
316A MSE 3.2 7.1 - - - +
317A ALA* 2.9 44.0 + - + +
319A MSE 3.9 10.3 - - + -
329A ALA 4.0 3.1 - - - -
330A ILE* 3.4 35.4 - - + -
333A GLY* 3.5 17.5 - - - -
334A TRP* 3.7 34.1 - + + -
337A LEU* 3.5 24.2 - - + +
348A LEU 3.9 1.6 - - - -
349A ALA* 4.4 2.7 - - + -
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Residues in contact with ASN 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.5 39.3 - - + +
271A LYS* 4.3 6.5 + - - -
272A PHE* 1.3 75.0 - - - +
274A LEU* 1.3 58.5 + - - +
314A LEU* 4.7 1.3 - - + -
315A ILE 3.5 4.3 - - - -
316A MSE 3.7 22.7 - - - +
334A TRP* 3.4 7.2 - - - -
347A LEU* 3.0 28.8 + - + +
348A LEU* 2.9 38.7 + - - +
350A GLN* 2.9 31.9 + - - +
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A PHE 5.0 0.2 - - - +
273A ASN* 1.3 73.6 - - - +
275A ALA* 1.3 59.7 + - - +
276A VAL* 3.5 20.8 + - + -
313A THR 3.5 1.0 - - - +
314A LEU* 3.8 2.8 - - - +
315A ILE* 2.7 51.3 + - + +
334A TRP* 4.0 18.2 - - + -
337A LEU* 4.2 22.0 - - + +
341A PHE* 3.6 39.7 - - + -
344A GLY* 3.7 7.6 - - - +
345A GLU 3.7 20.9 - - - +
346A PRO* 3.7 15.0 - - + -
347A LEU* 4.3 3.6 - - - -
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 3.4 29.4 - - + -
274A LEU* 1.3 69.4 - - - +
276A VAL* 1.3 62.1 + - - +
277A PRO* 3.5 2.4 - - - +
309A ARG* 5.3 1.1 - - - +
312A TYR* 4.0 9.7 - - + -
313A THR 3.7 5.6 - - - -
345A GLU* 3.0 46.2 + - + +
347A LEU* 3.5 21.2 - - + +
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU* 3.6 30.7 - - + -
275A ALA* 1.3 71.3 - - - +
277A PRO* 1.3 70.2 - - + +
281A ARG* 4.4 19.7 - - + +
312A TYR* 3.6 2.0 - - - -
313A THR* 2.8 63.4 + - + +
315A ILE* 3.8 17.5 - - + -
341A PHE* 4.1 17.5 - - + -
343A GLU 5.4 0.2 - - - -
344A GLY* 4.1 7.6 - - - +
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Residues in contact with PRO 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ALA 3.5 4.5 - - - +
276A VAL* 1.3 86.4 - - + +
278A GLY* 1.3 59.9 + - - +
281A ARG* 2.7 29.6 + - - -
311A GLY 3.8 2.0 - - - +
312A TYR* 3.3 28.3 - - + +
343A GLU* 3.1 36.6 - - + +
345A GLU* 3.5 9.6 - - - +
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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