Contacts of the strand formed by residues 292 - 301 (chain A) in PDB entry 3NGN
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 PHE 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PHE* 4.4 23.1 - + + -
234A ASP* 4.0 16.6 - - + -
235A ILE* 3.5 31.6 - - + -
287A PHE* 3.5 34.0 - - + -
288A LYS 2.9 13.8 + - - -
289A THR* 3.3 17.1 + - - +
291A LYS* 1.3 96.8 - - + +
293A THR* 1.3 64.6 + - - +
332A LEU* 4.2 21.5 - - + -
333A GLU 3.3 12.8 - - - +
334A VAL* 4.0 27.8 - - + -
335A HIS* 3.5 2.7 - - - -
338A LEU* 5.3 2.5 - - + -
354A LEU* 4.1 12.6 - - + -
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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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287A PHE* 4.6 0.4 - - - -
289A THR 4.8 0.2 + - - -
292A PHE* 1.3 72.2 + - - +
294A LEU* 1.3 73.2 + - - +
295A VAL* 3.5 2.9 + - + +
332A LEU* 3.3 3.5 - - - -
333A GLU* 2.6 59.6 + - - +
335A HIS* 2.6 27.3 + - - -
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Residues in contact with LEU 294 (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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260A ASP* 4.9 8.7 - - - +
261A GLY 5.8 2.5 - - - +
262A PHE* 5.6 4.0 - - + -
287A PHE* 3.6 28.9 - - + -
293A THR* 1.3 79.7 - - - +
295A VAL* 1.3 61.7 + - - +
296A GLN 3.5 28.5 - - - +
297A LYS* 4.1 27.8 - - + -
330A VAL* 3.7 22.2 - - + -
331A VAL 3.6 7.6 - - - +
332A LEU* 3.8 7.4 - - + -
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Residues in contact with VAL 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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293A THR* 3.6 17.3 - - + +
294A LEU* 1.3 77.7 - - - +
296A GLN* 1.3 71.2 + - + +
331A VAL* 2.7 26.0 + - + +
332A LEU 4.4 1.6 - - - -
333A GLU* 3.9 26.7 - - + +
351A LYS* 4.5 18.2 - - - +
353A LEU* 4.5 7.9 - - + -
389A ALA* 5.8 2.2 - - + -
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Residues in contact with GLN 296 (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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294A LEU* 3.5 8.6 - - - +
295A VAL* 1.3 87.3 - - + +
297A LYS* 1.3 59.9 + - - +
298A HIS* 3.6 25.9 - - + +
330A VAL* 3.3 3.1 - - - -
331A VAL* 2.7 47.5 + - + +
385A ILE 4.4 3.6 - - - +
388A LYS* 4.5 15.9 - - - +
389A ALA* 3.1 37.3 + - - +
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Residues in contact with LYS 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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262A PHE* 3.4 48.6 - - + -
294A LEU* 4.1 22.7 - - + -
296A GLN* 1.3 76.0 - - - +
298A HIS* 1.3 72.9 + - - +
329A ALA 3.5 4.7 - - - +
330A VAL* 4.4 5.4 - - + -
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Residues in contact with HIS 298 (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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262A PHE* 3.6 4.9 - - - -
296A GLN* 3.6 42.7 + - + +
297A LYS* 1.3 80.9 + - - +
299A THR* 1.3 65.9 + - - +
300A VAL* 5.1 2.0 - - + -
328A VAL* 3.3 4.2 - - - -
329A ALA* 2.8 44.3 + - + +
331A VAL* 4.9 1.0 - - - +
385A ILE* 3.5 50.8 - - + +
388A LYS* 6.2 2.3 - - + +
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Residues in contact with THR 299 (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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262A PHE* 3.4 12.1 - - - -
264A SER* 2.7 40.0 + - - +
265A PRO 5.3 0.7 - - - +
298A HIS* 1.3 74.2 - - - +
300A VAL* 1.3 71.4 + - - +
301A GLU* 4.1 17.1 + - - +
326A ILE* 5.0 6.1 - - + -
327A GLY 3.8 7.9 - - - +
328A VAL* 4.4 1.3 - - + +
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Residues in contact with VAL 300 (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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298A HIS* 5.1 2.9 - - + -
299A THR* 1.3 78.1 - - - +
301A GLU* 1.3 61.5 + - - +
302A PHE* 3.7 23.5 + - + -
305A VAL* 4.2 8.5 - - + -
326A ILE* 3.3 8.7 - - - +
327A GLY 3.0 35.7 + - - +
328A VAL* 5.7 1.1 - - - -
329A ALA* 5.9 0.4 - - + -
377A MET 5.3 0.2 - - - -
378A PHE* 4.2 19.7 - - + -
381A GLU* 3.9 40.8 - - + +
385A ILE* 4.7 17.0 - - + -
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Residues in contact with GLU 301 (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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265A PRO 4.4 4.0 - - - +
267A SER 4.3 4.7 + - - -
268A ARG* 3.4 56.2 + - - +
269A ALA 5.0 1.4 + - - -
299A THR* 4.1 13.5 + - - +
300A VAL* 1.3 72.6 - - - +
302A PHE* 1.3 65.1 + - - +
303A ASN* 3.2 21.5 - - - +
304A GLN* 3.2 24.1 + - + +
305A VAL* 3.1 24.4 + - - +
324A ASP* 5.5 1.6 - - - +
326A ILE* 3.7 21.6 - - + +
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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