Contacts of the helix formed by residues 262 - 275 (chain B) in PDB entry 3NJ8
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 HIS 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A ARG* 5.4 1.1 - - - +
23B TYR* 4.6 1.4 - - - -
227B LEU* 4.4 1.6 - - - -
259B ARG* 5.6 2.0 - - - +
260B ASP* 3.7 4.0 + - + +
261B LEU* 1.3 80.4 - - - +
263B SER* 1.3 101.1 + - - +
264B ASP* 2.9 25.3 + - + -
265B ASP* 3.2 34.8 + - - +
266B VAL 4.2 0.5 + - - -
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Residues in contact with SER 263 (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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21B HIS* 4.6 9.0 - - - -
22B GLY 4.6 2.5 - - - -
23B TYR* 3.6 3.3 - - - -
25B TRP* 5.8 2.4 - - - -
26B ALA* 3.5 25.6 - - - +
227B LEU* 3.8 34.9 - - - +
262B HIS* 1.3 88.0 + - - +
264B ASP* 1.3 83.0 + - - +
266B VAL* 3.2 18.2 + - - +
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Residues in contact with ASP 264 (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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279A ARG* 4.6 8.3 - - - +
26B ALA* 4.1 10.7 - - - +
29B LYS* 5.0 12.4 + - - +
30B HIS* 3.5 29.6 + - + +
262B HIS* 2.9 22.1 + - + -
263B SER* 1.3 85.5 + - - +
265B ASP* 1.3 58.4 + - - +
266B VAL 2.6 7.1 + - - -
267B GLY 2.2 29.4 + - - +
268B GLY 2.7 11.8 + - - -
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Residues in contact with ASP 265 (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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277A LEU 4.2 10.8 - - - +
279A ARG* 2.6 34.3 + - + +
280A ALA* 3.5 23.6 - - + +
281A VAL* 5.4 0.3 - - - +
259B ARG* 2.8 32.8 + - - -
261B LEU* 3.9 7.0 - - + +
262B HIS* 3.2 33.4 + - - +
264B ASP* 1.3 72.7 - - - +
266B VAL* 1.3 57.5 + - - +
268B GLY* 4.0 1.8 - - - +
269B ALA* 3.4 14.9 + - - +
288B VAL* 3.2 15.1 - - + +
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Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 3.2 48.9 - - + +
27B ILE* 4.5 8.1 - - + -
177B LEU* 3.9 26.2 - - + -
222B ILE* 4.1 6.0 - - + +
224B ALA* 3.7 21.3 - - + -
261B LEU* 5.2 4.3 - - + -
262B HIS 4.2 0.2 + - - -
263B SER 3.2 1.8 + - - +
264B ASP 2.6 4.2 + - - -
265B ASP* 1.3 74.2 - - - +
267B GLY* 1.3 54.4 + - - +
269B ALA* 3.5 3.2 + - - +
270B ALA* 2.7 32.9 + - - +
288B VAL* 4.1 17.7 - - + +
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Residues in contact with GLY 267 (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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26B ALA* 4.2 7.0 - - - +
27B ILE* 4.1 24.1 - - - -
30B HIS* 3.8 11.7 - - - +
263B SER 3.5 3.0 + - - -
264B ASP 2.2 19.7 + - - -
266B VAL* 1.3 67.0 - - - +
268B GLY* 1.3 52.7 + - - -
270B ALA* 3.0 7.6 + - - +
271B LEU* 2.7 35.5 + - - +
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Residues in contact with GLY 268 (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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277A LEU* 3.4 41.8 - - - +
279A ARG* 5.9 0.9 - - - -
30B HIS* 3.5 11.5 - - - -
264B ASP 2.7 14.5 + - - -
265B ASP* 4.2 2.5 - - - -
267B GLY* 1.3 73.8 - - - +
269B ALA* 1.3 62.8 + - - +
271B LEU* 2.9 16.7 + - - +
272B PHE 3.2 4.5 + - - -
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Residues in contact with ALA 269 (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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272A PHE* 3.9 18.6 - - + -
277A LEU 4.2 3.8 + - - -
281A VAL* 4.8 1.3 - - + -
222B ILE* 4.0 8.1 - - + -
265B ASP 3.4 14.2 + - - +
266B VAL 3.6 3.4 - - - +
268B GLY* 1.3 72.8 - - - +
270B ALA* 1.3 63.4 + - - +
272B PHE* 3.2 13.7 + - - +
273B LEU* 3.2 17.2 + - - +
286B LEU* 4.0 10.0 - - + +
288B VAL* 3.4 33.2 - - + -
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Residues in contact with ALA 270 (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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27B ILE* 3.6 34.5 - - + -
175B VAL* 4.9 5.2 - - + -
222B ILE* 3.8 15.6 - - + +
266B VAL 2.7 21.1 + - - +
267B GLY 3.0 4.2 + - - +
269B ALA* 1.3 68.4 - - - +
271B LEU* 1.3 71.2 + - - +
272B PHE 3.2 0.3 + - - -
273B LEU* 3.2 5.6 + - - +
274B LEU* 3.1 30.7 + - + +
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Residues in contact with LEU 271 (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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4A PRO* 4.0 17.0 - - + -
277A LEU* 4.0 11.2 - - + -
5B ILE* 3.9 28.5 - - + -
7B LEU* 3.5 32.3 - - + -
30B HIS* 4.1 29.8 - - + +
31B LEU* 3.9 16.8 - - + +
33B SER* 5.2 1.3 - - - +
34B ALA* 4.0 9.9 - - + -
267B GLY 2.7 15.5 + - - +
268B GLY* 3.1 11.0 - - - +
270B ALA* 1.3 70.5 - - - +
272B PHE* 1.3 63.9 + - - +
274B LEU* 2.9 7.0 + - - +
275B SER* 2.8 22.1 + - - -
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Residues in contact with PHE 272 (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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269A ALA* 4.0 24.9 - - + -
272A PHE* 3.5 62.4 - + + -
277A LEU* 4.6 2.6 - - + +
286A LEU* 4.1 15.7 - - + -
5B ILE* 5.1 2.9 - - + -
268B GLY 3.2 2.3 + - - +
269B ALA 3.2 8.3 - - - +
270B ALA 3.2 0.4 - - - -
271B LEU* 1.3 75.3 - - - +
273B LEU* 1.3 80.8 + - + +
274B LEU 2.7 5.4 + - - -
275B SER* 2.6 39.5 + - - +
277B LEU* 3.9 29.8 - - + -
278B ALA* 3.4 26.1 - - + +
281B VAL* 4.4 4.7 - - + -
286B LEU* 5.0 1.8 - - + -
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Residues in contact with LEU 273 (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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286A LEU* 5.3 1.3 - - + -
173B SER* 3.5 5.4 + - - -
174B ALA 6.1 0.2 - - - -
175B VAL* 4.1 17.7 - - + -
218B ARG* 2.9 28.8 + - - -
220B ASN* 4.2 23.4 + - + +
221B ALA 4.6 1.1 - - - +
222B ILE* 3.7 37.0 - - + -
269B ALA 3.2 8.7 + - - +
270B ALA 3.2 5.4 + - - +
272B PHE* 1.3 93.1 - - + +
274B LEU* 1.3 60.0 + - + +
275B SER 3.5 0.2 - - - -
278B ALA* 3.8 5.8 - - - -
281B VAL* 3.9 27.8 - - + -
284B VAL* 5.2 2.5 - - + -
286B LEU* 4.1 19.7 - - + -
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Residues in contact with LEU 274 (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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7B LEU* 3.6 14.4 - - - +
10B GLN* 4.8 1.7 - - - +
27B ILE* 4.3 0.2 - - + -
31B LEU* 3.9 19.3 - - + -
123B ILE* 3.3 36.5 - - + +
124B LEU 4.2 2.7 - - - +
125B VAL* 3.7 24.0 - - + -
173B SER* 3.2 38.8 + - - +
174B ALA 4.3 0.4 - - - +
175B VAL* 4.0 26.7 - - + -
218B ARG* 4.5 0.2 + - - -
270B ALA* 3.1 27.4 - - + +
271B LEU 2.9 5.6 + - - +
272B PHE 2.8 1.2 - - - -
273B LEU* 1.3 78.5 - - - +
275B SER* 1.3 60.2 + - - +
276B PRO* 4.6 0.2 - - - +
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Residues in contact with SER 275 (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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5B ILE* 3.2 35.4 - - - +
7B LEU* 3.8 3.6 - - - -
218B ARG* 3.3 13.7 + - - -
271B LEU 2.8 6.8 + - - -
272B PHE* 2.6 36.0 + - - +
274B LEU* 1.3 73.2 - - - +
276B PRO* 1.3 69.2 - - - +
277B LEU* 3.7 17.8 - - - +
278B ALA 3.0 11.8 + - - -
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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