Contacts of the helix formed by residues 283 - 295 (chain B) in PDB entry 3NNJ
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 ASP 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B HIS* 5.6 0.3 - - - -
119B GLY 4.1 13.0 - - - +
120B SER* 4.6 1.0 - - - +
122B SER* 4.7 0.9 + - - -
123B PHE* 5.3 1.0 - - - -
247B ARG* 3.0 40.0 + - - -
279B ARG 4.5 0.2 + - - -
280B TYR* 3.0 18.2 + - + +
282B LYS* 1.3 75.4 - - - +
284B SER* 1.3 61.2 + - - +
285B VAL 3.4 4.3 + - - -
286B LEU* 3.1 24.1 + - + +
287B VAL* 3.0 28.8 + - - +
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Residues in contact with SER 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 5.3 8.5 - - - -
69B ASP* 2.7 30.3 + - - -
70B LEU* 3.7 25.5 - - - +
99B HIS* 3.3 19.1 + - - -
282B LYS 3.4 6.6 + - - -
283B ASP* 1.3 72.4 + - - +
285B VAL* 1.3 60.7 + - - +
287B VAL* 3.7 7.4 - - - +
288B MSE 2.8 32.2 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.3 5.6 - - + -
98B MSE 4.5 12.6 - - + +
99B HIS* 3.5 37.7 - - + -
123B PHE* 3.8 37.9 - - + -
247B ARG* 3.6 19.5 - - - +
283B ASP* 3.3 5.5 + - - +
284B SER* 1.3 75.8 - - - +
286B LEU* 1.3 58.3 + - - +
288B MSE 3.6 13.2 - - + +
289B VAL* 2.8 41.8 + - + +
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Residues in contact with LEU 286 (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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122B SER* 4.4 13.2 - - - +
123B PHE* 4.9 11.2 - - + -
260B LEU* 3.5 31.4 - - + -
263B PHE* 4.2 20.9 - - + -
280B TYR* 3.7 45.1 - - + +
281B ASN* 5.6 1.3 - - - +
283B ASP* 3.1 27.8 + - + +
285B VAL* 1.3 81.0 - - - +
287B VAL* 1.3 63.8 + - + +
290B SER* 2.8 36.3 + - - +
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 6.5 1.1 - - - -
280B TYR 4.8 0.4 - - - +
281B ASN* 3.2 38.8 - - + +
283B ASP 3.0 17.2 + - - +
284B SER* 3.7 9.9 - - - +
285B VAL 3.2 0.2 - - - -
286B LEU* 1.3 76.5 - - + +
288B MSE 1.3 65.4 + - - +
290B SER* 3.2 6.3 + - - -
291B ARG* 3.0 60.4 + - + +
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Residues in contact with MSE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.8 33.9 - - + -
98B MSE 5.4 9.9 - - - +
284B SER 2.8 19.5 + - - +
285B VAL* 3.6 18.2 - - + +
287B VAL* 1.3 79.2 - - - +
289B VAL* 1.3 69.1 + - + +
291B ARG* 3.5 6.6 + - - +
292B ALA* 3.2 21.5 + - - +
305B ILE* 4.0 25.6 - - - -
307B HIS* 4.0 26.7 - - + +
308B VAL* 4.1 16.2 - - + -
315B ARG* 5.0 3.6 - - - +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B MSE 6.3 1.1 - - - -
123B PHE* 4.1 15.0 - - + -
255B VAL* 3.7 32.3 - - + -
260B LEU* 3.8 7.9 - - + -
285B VAL* 2.8 39.0 + - + +
286B LEU 4.4 1.3 - - - +
288B MSE 1.3 80.9 - - + +
290B SER* 1.3 62.3 + - - +
292B ALA* 3.3 3.1 + - - +
293B VAL* 3.0 21.6 + - + +
302B LEU* 4.0 18.2 - - + -
305B ILE* 3.9 22.9 - - + -
308B VAL* 6.2 0.2 - - + -
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Residues in contact with SER 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 3.8 22.1 + - - +
263B PHE* 5.9 1.2 - - - +
264B SER* 5.6 5.3 + - - -
286B LEU* 2.8 37.6 + - - +
287B VAL* 3.2 5.4 + - - -
289B VAL* 1.3 77.9 - - - +
291B ARG* 1.3 58.0 + - - +
293B VAL* 3.1 4.5 + - - +
294B GLN* 2.9 30.0 + - - +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 5.3 15.0 - - - +
287B VAL* 3.0 44.0 + - + +
288B MSE 3.9 5.6 - - - +
290B SER* 1.3 72.1 - - - +
292B ALA* 1.3 67.7 + - - +
293B VAL 3.1 0.2 + - - -
294B GLN* 3.2 11.2 + - - +
295B LYS* 2.9 30.8 + - - +
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Residues in contact with ALA 292 (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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288B MSE 3.2 11.5 + - - +
289B VAL 3.6 7.9 - - - +
291B ARG* 1.3 80.8 - - - +
293B VAL* 1.3 64.2 + - - +
295B LYS* 3.4 10.2 + - - +
296B GLY 3.2 22.7 + - - +
297B LEU* 3.8 9.5 - - + +
305B ILE* 4.0 34.3 - - + -
306B PRO* 5.0 5.8 - - + -
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B VAL* 4.0 12.6 - - + -
257B GLU* 3.7 30.7 - - + +
260B LEU* 3.7 24.9 - - + -
289B VAL* 3.0 19.2 + - + +
290B SER* 3.4 9.0 - - - +
291B ARG 3.1 0.2 - - - -
292B ALA* 1.3 76.1 - - - +
294B GLN* 1.3 57.3 + - - +
296B GLY* 2.7 26.0 + - - -
297B LEU* 3.9 25.4 + - + -
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Residues in contact with GLN 294 (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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290B SER 2.9 15.4 + - - +
291B ARG* 3.8 9.8 - - - +
293B VAL* 1.3 74.9 - - - +
295B LYS* 1.3 59.8 + - - +
296B GLY* 2.8 11.4 + - - -
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Residues in contact with LYS 295 (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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291B ARG* 2.9 21.3 + - - +
292B ALA* 3.7 9.0 - - - +
294B GLN* 1.3 75.6 - - - +
296B GLY* 1.3 61.3 + - - +
306B PRO* 6.4 2.5 - - + -
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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