Contacts of the strand formed by residues 289 - 297 (chain A) in PDB entry 4NAM
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 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ILE* 4.0 1.4 - - - +
270A ILE* 3.3 2.5 - - - -
271A LEU* 2.8 50.8 + - + +
288A THR* 1.3 76.8 - - - +
290A SER* 1.3 62.8 + - - +
291A LYS* 4.2 27.1 - - + -
339A SER* 5.6 0.7 - - - +
340A LEU* 4.3 10.8 - - + -
346A FTR 3.7 44.4 - - + +
349A THR* 3.9 15.3 - - + -
350A MET* 3.3 37.2 - - + -
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Residues in contact with SER 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ILE 3.4 8.3 - - - -
270A ILE* 3.4 27.3 - - - +
288A THR* 4.2 5.0 + - - -
289A ILE* 1.3 72.8 - - - +
291A LYS* 1.3 70.9 + - - +
339A SER* 4.2 12.3 + - - -
340A LEU* 5.8 1.4 - - - +
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Residues in contact with LYS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ASN* 3.4 3.1 - - - +
269A ILE* 2.9 40.2 + - + +
289A ILE* 4.2 19.5 - - + -
290A SER* 1.3 82.0 - - - +
292A ASN* 1.3 68.8 + - - +
334A ILE* 3.8 25.6 - - + -
335A ASP* 3.5 23.8 + - + +
336A HIS* 4.6 3.9 + - - +
337A SER 3.0 22.7 + - - +
338A LEU* 4.8 0.6 - - - +
339A SER* 2.6 30.2 + - - +
346A FTR 4.9 16.4 - - + -
446A LYS* 5.9 1.8 - - - +
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Residues in contact with ASN 292 (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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267A GLU 3.9 6.7 - - - +
268A ASN* 3.8 17.0 + - - +
291A LYS* 1.3 76.6 - - - +
293A THR* 1.3 63.0 + - - +
335A ASP* 3.0 43.6 + - + +
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Residues in contact with THR 293 (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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266A MET* 2.8 30.4 + - - +
267A GLU* 3.0 28.1 + - - +
268A ASN* 3.1 2.9 + - - -
269A ILE* 3.7 32.8 - - + -
292A ASN* 1.3 82.5 - - - +
294A SER* 1.3 60.9 + - - +
332A VAL* 3.6 18.2 - - + -
333A ALA 3.2 12.8 - - - +
334A ILE* 4.0 12.6 - - + -
335A ASP 4.7 0.2 - - - +
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Residues in contact with SER 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A THR* 1.3 73.6 - - - +
295A THR* 1.3 64.8 + - - +
296A SER* 5.1 3.1 + - - -
331A THR 3.7 1.4 - - - +
332A VAL* 3.5 0.7 - - - -
333A ALA* 2.8 46.0 + - - +
703A LYS* 5.0 9.8 + - - -
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Residues in contact with THR 295 (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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263A HIS* 4.9 3.6 + - + -
264A VAL 3.4 25.8 - - - +
265A ASP* 3.2 25.0 + - + +
266A MET* 2.8 34.0 + - - +
294A SER* 1.3 76.7 + - - +
296A SER* 1.3 69.1 + - - +
330A SER* 3.7 16.6 - - - +
331A THR 3.3 8.1 - - - +
332A VAL* 3.5 13.8 - - + +
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A HIS* 4.8 1.3 - - - -
294A SER* 5.1 3.5 + - - -
295A THR* 1.3 78.5 + - - +
297A ARG* 1.3 66.9 + - - +
298A THR* 3.5 3.1 - - - +
330A SER* 3.9 4.5 - - - -
331A THR 2.9 32.4 + - - -
499A ASN* 4.6 13.0 + - - -
603A ILE* 3.8 36.2 - - - +
637A LYS* 5.5 3.8 - - - -
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Residues in contact with ARG 297 (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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261A ILE* 3.8 21.7 - - - +
262A VAL 5.6 0.2 - - - -
263A HIS* 3.3 48.2 + - + +
296A SER* 1.3 78.1 - - - +
298A THR* 1.3 73.0 + - - +
299A HIS* 5.8 1.2 - - - +
327A SER 5.0 6.7 + - - -
328A ASN* 4.9 6.9 + - - +
329A SER 3.5 16.6 - - - +
330A SER* 4.0 2.7 - - - -
369A THR* 3.9 16.8 + - - -
492A ILE* 4.6 6.1 - - - +
499A ASN* 6.5 0.4 - - + -
500A LEU* 3.0 64.6 + - + +
501A VAL 4.1 0.2 - - - -
502A GLU* 3.8 30.7 + - - +
603A ILE* 4.5 2.6 - - - +
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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