Contacts of the strand formed by residues 327 - 340 (chain A) in PDB entry 3NDF
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 LEU 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 5.0 2.2 - - + -
181A VAL* 3.3 48.2 - - + -
182A PHE* 4.1 18.6 - - + -
316A ALA* 4.0 11.3 - - - +
318A LEU* 3.6 31.9 - - + +
321A VAL* 5.3 3.6 - - + -
322A THR* 3.6 28.9 - - + +
325A ALA* 3.5 15.8 + - + +
326A PRO* 1.3 82.4 - - - +
328A LYS* 1.3 65.2 + - - +
355A ALA* 4.8 2.9 - - + -
356A ILE 3.4 5.6 - - - +
357A PRO* 4.2 9.9 - - + -
358A ARG* 3.7 7.5 - - - +
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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
----------------------------------------------------------
311A VAL 3.8 3.1 - - - +
312A PHE 3.9 16.2 + - - +
313A SER* 3.5 14.1 - - - +
314A ASN* 4.2 12.5 - - - +
316A ALA* 3.7 14.6 - - + -
318A LEU* 3.6 11.4 - - - -
327A LEU* 1.3 79.2 - - - +
329A LEU* 1.3 63.0 + - - +
330A SER* 5.8 0.9 - - - +
355A ALA* 3.1 2.7 - - - -
356A ILE* 2.6 62.1 + - + +
357A PRO 4.1 4.7 - - - -
358A ARG* 3.5 40.2 + - + +
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 4.0 22.9 - - + -
64A LEU* 4.1 19.7 - - + -
182A PHE* 4.6 7.6 - - + -
311A VAL* 3.0 22.4 + - + +
312A PHE* 3.1 57.2 - - + +
318A LEU* 4.2 3.6 - - + +
328A LYS* 1.3 74.7 - - - +
330A SER* 1.3 59.7 + - - +
331A LYS 4.1 6.5 - - - +
353A ASP* 4.0 18.8 - - + +
354A GLU 3.2 28.5 - - - +
355A ALA* 4.1 9.4 - - + +
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Residues in contact with SER 330 (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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300A LYS* 5.0 6.8 - - - +
312A PHE* 4.4 7.9 - - - -
328A LYS* 3.7 2.6 + - - +
329A LEU* 1.3 73.9 - - - +
331A LYS* 1.3 70.8 + - - +
354A GLU* 3.0 14.6 + - - +
356A ILE* 3.4 41.1 - - - +
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Residues in contact with LYS 331 (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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175A GLU 5.6 4.0 - - - +
298A ASP* 4.3 10.5 - - - +
300A LYS* 5.4 0.9 - - - -
312A PHE* 4.3 4.4 - - - -
329A LEU* 3.6 3.9 - - - +
330A SER* 1.3 90.5 + - - +
332A ALA* 1.3 62.3 + - - +
333A VAL* 3.7 27.1 - - + -
352A ASP 3.7 0.7 - - - +
353A ASP* 3.4 3.8 - - - -
354A GLU* 3.0 56.3 + - + +
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Residues in contact with ALA 332 (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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61A PHE* 4.0 11.9 - - + -
298A ASP* 3.4 9.8 + - - +
299A LEU* 2.8 34.3 + - + +
300A LYS* 4.0 11.8 - - - +
312A PHE* 3.9 26.1 - - + -
329A LEU* 4.8 0.2 - - + -
331A LYS* 1.3 75.6 - - - +
333A VAL* 1.3 62.6 + - - +
353A ASP* 3.5 16.8 - - - +
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Residues in contact with VAL 333 (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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172A LEU* 3.6 34.8 - - + +
296A THR* 5.7 5.4 - - + -
297A TYR 3.8 8.1 - - - +
298A ASP* 5.1 3.6 - - + +
299A LEU* 5.1 0.2 - - - -
331A LYS* 3.7 31.2 - - + -
332A ALA* 1.3 74.3 - - - +
334A HIS* 1.3 68.5 + - - +
335A LYS* 5.3 0.4 - - + -
351A ASP* 3.3 6.4 - - - +
352A ASP* 2.7 56.4 + - + +
353A ASP* 4.0 1.2 + - - +
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Residues in contact with HIS 334 (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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52A PHE* 3.2 22.4 - - + +
53A SER* 3.0 41.6 + - - -
56A SER* 4.6 0.2 - - - -
57A ILE* 3.3 18.4 - - + +
296A THR* 3.6 3.1 - - - +
297A TYR* 3.0 45.2 + + + +
299A LEU* 3.5 25.1 - - + -
332A ALA 3.9 0.6 + - - -
333A VAL* 1.3 77.9 - - - +
335A LYS* 1.3 70.4 + - - +
336A ALA* 3.9 6.0 - - + +
350A ALA 3.5 13.2 + - - -
351A ASP* 2.9 25.3 + - - +
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Residues in contact with LYS 335 (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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168A LYS 5.6 0.7 - - - -
169A ILE* 3.8 27.2 - - + +
170A VAL 4.7 12.1 + - - +
171A ASP 5.8 1.0 + - - +
172A LEU* 4.0 22.9 - - + +
294A THR* 3.8 23.0 - - - +
295A GLY 3.3 11.4 - - - +
296A THR* 3.7 19.2 + - + +
334A HIS* 1.3 79.6 + - - +
336A ALA* 1.3 66.1 + - - +
337A VAL* 4.1 11.4 - - + -
349A GLY* 3.4 1.6 - - - -
350A ALA* 2.9 33.1 + - + +
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Residues in contact with ALA 336 (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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51A PHE* 3.6 25.3 - - + +
52A PHE* 3.7 25.6 - - - -
53A SER 4.4 0.2 - - - +
169A ILE* 4.7 0.4 - - - -
294A THR* 3.6 0.7 - - - +
295A GLY 2.9 33.0 + - - +
334A HIS* 3.9 4.0 + - - +
335A LYS* 1.3 75.4 - - - +
337A VAL* 1.3 66.9 + - - +
348A ALA 3.0 12.3 - - - +
349A GLY* 4.2 3.8 - - - -
384B PHE* 4.9 0.9 - - + -
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PHE* 3.5 3.8 - - - -
168A LYS* 3.9 30.1 - - + +
169A ILE* 4.0 4.7 - - + -
293A ILE 3.9 2.7 - - - -
294A THR* 3.8 25.1 - - + +
335A LYS* 4.1 14.6 - - - -
336A ALA* 1.3 79.9 - - - +
338A LEU* 1.3 60.5 + - - +
339A THR* 5.4 1.8 - - - +
346A GLU* 3.9 1.3 - - + +
347A ALA* 3.1 5.9 - - - -
348A ALA* 2.7 58.5 + - + +
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Residues in contact with LEU 338 (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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51A PHE* 3.3 32.5 - - + -
291A LEU* 3.5 25.1 - - + -
292A SER* 3.4 6.2 + - - -
293A ILE* 3.0 38.3 + - + +
337A VAL* 1.3 73.7 - - - +
339A THR* 1.3 71.2 + - - +
340A ILE* 3.6 9.0 - - + -
345A THR* 3.5 29.2 - - + -
346A GLU 3.6 2.7 - - - +
347A ALA* 4.3 0.7 - - + -
372B PHE* 3.4 36.3 - - + -
374B MET* 4.2 7.6 - - - -
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Residues in contact with THR 339 (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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290A LYS* 6.5 0.9 - - - -
291A LEU 3.6 8.1 - - - +
292A SER* 4.7 9.6 + - - +
337A VAL* 5.4 2.1 - - - +
338A LEU* 1.3 76.7 + - - +
340A ILE* 1.3 67.6 + - - +
341A ASP* 4.3 16.7 + - + +
345A THR* 3.3 7.1 - - - +
346A GLU* 2.7 57.7 + - + +
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Residues in contact with ILE 340 (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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194A TRP* 4.0 17.7 - - + -
221A MET* 4.0 19.5 - - + -
244A TYR* 5.4 0.9 - - - +
252A PHE* 4.3 22.9 - - + -
288A LEU* 4.7 5.2 - - + -
289A PRO 4.5 5.6 - - - +
290A LYS* 3.4 7.8 - - - +
291A LEU* 2.9 62.7 + - + +
338A LEU* 3.6 23.6 - - + -
339A THR* 1.3 80.0 - - - +
341A ASP* 1.3 63.9 + - - +
344A GLY 3.8 2.7 - - - -
345A THR* 3.8 12.8 - - + +
372B PHE* 4.9 5.2 - - + -
374B MET* 6.1 0.9 - - + -
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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