Contacts of the strand formed by residues 347 - 354 (chain B) in PDB entry 3N9V
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 347 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B PHE 3.7 5.2 - - - +
302B GLN* 5.0 0.9 - - + -
343B ARG* 3.2 2.5 - - - -
344B LEU* 2.9 36.3 + - + +
345B VAL 3.5 0.4 - - - -
346B GLY* 1.3 79.7 - - - +
348B MET* 1.3 58.7 + - - +
378B GLY 4.0 12.8 - - - +
379B ASN 4.8 1.3 - - - +
380B LYS* 4.0 8.5 - - - +
381B GLY 3.7 32.5 - - - +
382B GLY* 4.5 0.9 - - - +
383B VAL* 3.4 18.8 - - + +
398B ASN* 3.7 37.7 - - - +
400B HIS* 3.8 30.5 - - + +
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Residues in contact with MET 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B VAL 3.9 1.1 - - - +
300B GLY* 3.3 0.9 - - - -
301B PHE* 2.8 64.9 + - + +
304B LEU* 3.5 31.6 - - + -
319B GLU* 4.0 33.7 - - - +
322B TRP* 4.1 6.7 - - + -
323B PHE 4.4 4.7 - - - +
341B LEU* 4.2 13.2 - - + -
342B ILE 3.3 10.5 - - - +
343B ARG* 4.0 16.6 - - + +
346B GLY 3.6 1.4 + - - +
347B ILE* 1.3 76.4 - - - +
349B LEU* 1.3 68.6 + - - +
350B LEU* 4.3 12.3 - - + -
383B VAL* 4.5 0.2 - - - -
398B ASN* 3.0 5.6 + - - -
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B CYS* 4.4 0.4 - - + -
299B VAL 3.3 31.2 - - - +
300B GLY* 3.8 7.6 - - - +
341B LEU* 3.5 3.3 - - - -
342B ILE* 2.9 33.9 + - + -
348B MET* 1.3 74.8 - - - +
350B LEU* 1.3 65.4 + - - +
383B VAL* 3.7 16.7 - - + +
384B ALA* 4.4 2.5 - - - -
385B ILE* 3.7 24.7 - - + +
396B VAL* 3.3 50.7 - - + +
398B ASN* 4.1 17.0 - - + +
445B LEU* 4.3 6.1 - - + -
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B TYR 3.7 0.7 - - - +
298B CYS* 3.4 4.9 - - - +
299B VAL* 2.9 37.4 + - + +
301B PHE* 4.3 10.8 - - + -
323B PHE* 3.6 27.6 - - + -
326B VAL* 4.0 26.2 - - + -
338B LYS* 5.5 0.9 - - + -
340B LYS 3.4 3.6 - - - +
341B LEU* 3.5 35.7 - - + -
348B MET* 4.3 12.6 - - + -
349B LEU* 1.3 78.9 - - - +
351B LEU* 1.3 59.4 + - - +
352B TYR* 3.7 31.6 - - + +
385B ILE* 4.3 2.2 - - - -
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B VAL* 3.6 23.8 - - + -
297B TYR 3.3 13.9 - - - +
298B CYS* 3.7 16.2 - - + -
338B LYS* 3.7 3.6 - - - +
339B VAL* 2.8 57.2 + - + -
340B LYS* 2.8 15.1 + - + +
350B LEU* 1.3 74.5 - - - +
352B TYR* 1.3 56.2 + - - +
353B VAL* 4.9 1.1 - - + -
385B ILE* 4.0 24.0 - - + +
387B PHE* 3.4 43.3 - - + -
396B VAL* 5.2 1.8 - - + -
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Residues in contact with TYR 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A PRO* 5.3 5.2 - - + -
296B VAL* 3.4 2.1 - - - +
297B TYR* 2.7 59.9 + - + +
299B VAL* 4.9 2.2 - - + -
323B PHE* 3.4 32.3 + + - -
326B VAL* 3.3 33.5 - - + +
327B SER* 3.0 27.9 + - - -
330B LEU* 3.5 21.1 - - + -
336B TYR* 4.2 14.4 - - + -
337B ALA 3.2 9.6 - - - +
338B LYS* 4.0 19.7 - - + -
339B VAL* 4.3 0.7 - - - +
350B LEU* 3.7 18.4 - - + +
351B LEU* 1.3 75.7 - - - +
353B VAL* 1.3 68.6 + - - +
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ASP 3.4 8.3 - - - +
296B VAL* 3.9 24.0 - - + -
336B TYR* 3.5 7.0 - - - -
337B ALA* 2.8 33.5 + - + +
339B VAL* 3.8 21.1 - - + +
351B LEU* 4.9 2.7 - - + -
352B TYR* 1.3 80.1 - - - +
354B LYS* 1.3 75.6 + - - +
357B HIS* 4.2 7.0 - - + -
358B ALA* 3.9 26.0 - - + +
361B ILE* 4.0 24.2 - - + -
389B PHE* 6.0 0.2 - - + -
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Residues in contact with LYS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ALA* 3.7 17.7 + - - +
294B PRO 3.4 27.4 - - - +
295B ASP* 3.1 33.9 + - - +
334B ALA* 3.9 22.4 - - + -
335B LYS 3.6 3.8 - - - +
336B TYR* 3.3 17.3 - - + -
353B VAL* 1.3 74.3 - - - +
355B GLN* 1.3 67.3 + - - +
356B GLU* 3.7 25.9 + - + +
357B HIS* 2.9 26.6 + - + +
358B ALA 3.5 5.2 + - - -
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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