Contacts of the strand formed by residues 322 - 328 (chain A) in PDB entry 3N2Q
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 ILE 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A GLN* 3.9 34.5 - - + +
316A ILE 3.8 5.4 - - - +
317A LYS* 4.1 22.4 - - + +
321A LYS* 1.3 73.1 - - - +
323A GLU* 1.3 61.9 + - - +
324A ALA 3.9 7.6 - - - +
325A VAL* 3.8 28.5 - - + -
340A LEU* 3.6 25.5 - - - +
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Residues in contact with GLU 323 (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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283A ILE* 6.1 0.7 - - + -
285A TYR* 3.5 38.9 + - + +
291A LEU* 3.8 15.7 - - + -
316A ILE* 2.7 18.6 + - + +
317A LYS 5.2 0.2 - - - -
318A SER* 3.4 26.3 + - - +
321A LYS* 3.1 42.1 + - - +
322A ILE* 1.3 73.7 - - - +
324A ALA* 1.3 61.2 + - - +
339A PHE* 3.6 6.9 - - - +
340A LEU* 3.1 32.4 + - - +
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Residues in contact with ALA 324 (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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291A LEU* 4.2 9.2 - - + -
295A THR* 4.2 17.0 - - + -
314A LEU 3.9 0.8 - - - +
315A GLN* 3.6 0.2 - - - -
316A ILE* 2.8 36.0 + - + +
322A ILE* 3.9 1.1 - - - +
323A GLU* 1.3 81.0 - - - +
325A VAL* 1.3 65.5 + - - +
326A ILE 4.3 0.2 - - - -
337A VAL* 4.4 2.2 - - + -
338A SER 3.2 13.2 - - - +
339A PHE* 3.7 23.3 - - + -
340A LEU 4.9 0.2 - - - +
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Residues in contact with VAL 325 (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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198A LEU* 3.8 22.7 - - + +
313A GLN* 3.6 36.3 - - + +
314A LEU 3.3 10.5 - - - +
315A GLN* 4.3 8.7 - - + +
322A ILE* 3.8 20.0 - - + -
324A ALA* 1.3 80.3 - - - +
326A ILE* 1.3 65.3 + - - +
327A ILE* 3.9 10.1 + - + +
336A PHE* 3.6 2.3 - - - +
337A VAL* 3.6 2.4 - - - -
338A SER* 3.0 32.8 + - - +
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Residues in contact with ILE 326 (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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295A THR* 3.4 42.0 - - + +
298A ALA* 3.7 22.4 - - + -
299A ALA* 4.0 9.0 - - + +
302A MSE 3.6 30.5 - - + +
312A VAL 3.9 0.3 - - - +
313A GLN* 3.3 2.3 - - - -
314A LEU* 2.9 40.0 + - + +
316A ILE* 4.7 6.1 - - + -
325A VAL* 1.3 75.7 - - - +
327A ILE* 1.3 67.0 + - - +
335A PRO* 3.9 16.4 - - + -
336A PHE 3.4 7.0 - - - +
337A VAL* 4.0 14.6 - - + -
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Residues in contact with ILE 327 (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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198A LEU* 3.3 54.3 - - + +
311A LYS* 3.8 20.6 - - - +
312A VAL 3.5 2.9 - - - +
313A GLN* 3.7 20.2 - - + +
325A VAL* 3.9 8.3 - - + +
326A ILE* 1.3 82.4 - - - +
328A LYS* 1.3 62.2 + - - +
329A GLU* 4.0 16.8 + - - +
332A SER* 5.3 0.3 + - - -
334A LYS 4.7 0.3 - - - +
335A PRO* 3.2 4.3 - - - +
336A PHE* 2.9 61.8 + - + +
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Residues in contact with LYS 328 (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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302A MSE 4.6 17.7 - - + +
303A LEU* 4.2 17.7 - - + -
306A LEU 5.4 1.1 - - - +
307A PRO 4.0 10.3 - - - -
308A LYS* 2.7 37.7 + - - +
310A ALA 3.4 19.5 - - - -
311A LYS* 3.6 0.9 - - - +
312A VAL* 2.9 50.4 + - + +
326A ILE 4.3 0.2 - - - -
327A ILE* 1.3 73.2 - - - +
329A GLU* 1.3 74.6 + - - +
330A LYS 3.6 0.2 + - - -
332A SER* 3.9 27.6 + - - +
335A PRO* 4.0 23.3 - - + -
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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
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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