Contacts of the helix formed by residues 256 - 275 (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 256 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B SER 4.5 1.6 - - - +
123B PHE 3.4 6.5 + - - -
124B THR 3.8 19.3 - - - +
125B LYS* 4.0 22.0 + - + +
126B THR 4.9 0.5 + - - -
166B ASP* 4.8 1.9 - - - +
255B VAL* 1.3 77.9 - - - +
257B GLU* 1.3 61.9 + - - +
258B GLU* 3.0 14.4 + - - +
259B ARG* 2.9 51.9 + - + +
260B LEU* 3.2 24.8 + - - +
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Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS* 5.7 1.0 - - - +
255B VAL* 3.9 9.5 + - + +
256B ASP* 1.3 73.1 + - - +
258B GLU* 1.3 60.1 + - + +
260B LEU* 3.2 8.5 + - - +
261B GLY* 2.8 24.9 + - - -
293B VAL* 3.7 36.5 - - + +
297B LEU* 4.0 23.5 + - + +
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Residues in contact with GLU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LYS* 6.2 0.3 - - - +
125B LYS* 5.3 6.9 + - - +
170B LYS* 5.7 5.0 - - - -
256B ASP* 3.0 7.8 + - - +
257B GLU* 1.3 76.9 - - + +
259B ARG* 1.3 66.2 + - - +
261B GLY* 3.0 4.6 + - - +
262B LEU* 2.9 28.8 + - + +
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Residues in contact with ARG 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL 5.0 3.3 + - - -
121B PHE 4.0 1.4 + - - -
122B SER* 2.7 56.4 + - - +
124B THR 2.9 21.6 + - - -
126B THR* 2.8 29.5 + - - +
162B TYR* 5.2 8.8 - - - +
165B PHE* 5.3 2.4 - - - -
166B ASP* 2.9 34.6 + - - +
169B LEU* 3.8 21.8 - - + -
256B ASP* 2.9 38.2 + - - +
258B GLU* 1.3 75.6 - - - +
260B LEU* 1.3 64.3 + - + +
262B LEU* 2.9 23.0 + - + +
263B PHE* 3.0 22.5 + - + -
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B SER 4.4 12.3 - - - +
123B PHE* 4.5 4.5 - - - -
255B VAL* 4.0 6.1 - - + -
256B ASP 3.2 12.0 + - - +
257B GLU* 3.2 8.9 + - - +
258B GLU 3.2 0.4 - - - -
259B ARG* 1.3 79.5 - - - +
261B GLY* 1.3 61.1 + - - +
263B PHE* 3.4 10.3 + - + +
264B SER* 3.1 26.7 + - - -
286B LEU* 3.5 29.6 - - + -
289B VAL* 3.8 20.6 - - + -
290B SER* 3.8 22.3 + - - +
293B VAL* 3.7 33.2 - - + -
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Residues in contact with GLY 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLU 2.8 14.8 + - - -
258B GLU* 3.0 5.8 + - - -
260B LEU* 1.3 77.3 - - - +
262B LEU* 1.3 62.7 + - - +
264B SER* 3.4 6.6 + - - -
265B LYS* 3.0 24.9 + - - +
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASP* 4.5 7.4 - - + +
169B LEU* 4.0 35.7 - - + +
170B LYS* 3.8 37.5 - - + -
173B ILE* 3.6 32.9 - - + +
258B GLU* 2.9 20.1 + - + +
259B ARG* 2.9 12.8 + - + +
261B GLY* 1.3 76.4 - - - +
263B PHE* 1.3 57.1 + - - +
265B LYS* 3.3 3.7 + - - +
266B TYR* 2.9 29.2 + - - +
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Residues in contact with PHE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLY* 5.8 2.0 - - - -
122B SER* 3.4 35.7 - - - -
165B PHE* 4.7 8.5 - + - -
169B LEU* 3.9 35.9 - - + -
259B ARG* 3.0 28.3 + - + -
260B LEU* 3.8 21.1 - - + +
262B LEU* 1.3 73.0 - - - +
264B SER* 1.3 55.1 + - - +
266B TYR* 3.1 3.4 + - + -
267B SER* 2.7 34.4 + - - -
280B TYR* 2.8 50.9 + + + +
286B LEU* 4.2 15.5 - - + -
290B SER* 5.9 1.1 - - - +
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Residues in contact with SER 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU 3.1 14.4 + - - -
261B GLY* 3.6 9.5 - - - -
263B PHE* 1.3 74.1 - - - +
265B LYS* 1.3 65.3 + - - +
267B SER* 3.0 17.2 + - - -
268B GLN* 3.0 21.1 + - - +
290B SER* 5.6 4.9 + - - -
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Residues in contact with LYS 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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173B ILE* 3.9 38.1 - - + -
261B GLY 3.0 15.5 + - - +
262B LEU* 3.6 4.9 - - - +
263B PHE 3.2 0.2 - - - -
264B SER* 1.3 80.5 - - - +
266B TYR* 1.3 62.1 + - - +
268B GLN* 3.5 20.8 + - + +
269B LEU* 3.2 44.8 + - - +
272B ARG* 5.7 1.4 - - - +
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Residues in contact with TYR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ASN* 4.0 37.2 - - + -
173B ILE* 3.8 11.1 - - + +
182B LEU* 3.8 33.8 - - + +
183B ASN* 3.7 19.2 + - - -
186B VAL* 4.1 12.3 - - + +
262B LEU 2.9 17.6 + - - +
263B PHE* 3.6 6.3 - + + +
265B LYS* 1.3 77.2 - - - +
267B SER* 1.3 57.8 + - - +
269B LEU* 3.3 8.1 + - + +
270B HIS* 3.0 35.9 + + - +
278B PRO* 4.0 16.4 - - + -
280B TYR* 3.3 27.4 - + - +
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Residues in contact with SER 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B PHE 2.7 17.3 + - - -
264B SER* 3.0 9.2 + - - -
266B TYR* 1.3 74.9 - - - +
268B GLN* 1.3 57.8 + - - +
270B HIS* 3.7 1.4 - - - +
271B SER* 2.9 28.7 + - - -
277B LEU* 4.1 10.4 - - - +
278B PRO* 3.5 16.4 - - - +
280B TYR* 3.0 28.1 + - - -
281B ASN* 3.5 12.8 + - - -
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Residues in contact with GLN 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B SER* 3.0 12.9 + - - +
265B LYS* 3.7 34.0 + - + +
266B TYR 3.3 0.2 - - - -
267B SER* 1.3 73.5 - - - +
269B LEU* 1.3 68.0 + - + +
271B SER* 3.3 6.5 + - - -
272B ARG* 2.8 31.3 + - + +
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Residues in contact with LEU 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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172B ASN 4.3 4.7 - - - +
173B ILE* 3.8 38.8 - - + +
175B TRP* 4.1 32.9 - - + +
182B LEU* 4.1 7.2 - - + +
265B LYS* 3.2 33.2 + - - +
266B TYR* 3.8 10.5 - - + +
268B GLN* 1.3 80.0 - - + +
270B HIS* 1.3 63.5 + - - +
272B ARG* 3.5 37.8 + - - +
273B TYR* 3.1 26.2 + - - +
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Residues in contact with HIS 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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182B LEU* 3.6 11.2 - - + +
183B ASN* 4.4 8.2 + - - -
266B TYR* 3.0 36.9 + + + +
267B SER 3.7 1.3 - - - +
268B GLN 3.1 0.2 - - - -
269B LEU* 1.3 79.5 - - - +
271B SER* 1.3 57.2 + - - +
273B TYR 3.2 0.3 + - - -
274B TYR* 2.7 54.6 + + - +
276B THR* 2.9 46.5 + - + -
277B LEU 3.6 2.5 - - - -
278B PRO* 3.5 38.8 - - + +
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Residues in contact with SER 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B SER 2.9 16.6 + - - -
268B GLN* 3.3 7.1 + - - -
270B HIS* 1.3 75.0 - - - +
272B ARG* 1.3 64.4 + - - +
273B TYR 3.0 1.8 - - - -
275B LYS* 2.6 35.1 + - - +
276B THR* 2.8 24.4 + - - +
277B LEU* 3.7 16.4 - - - +
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Residues in contact with ARG 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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175B TRP* 3.7 16.6 + - - -
176B ASP* 4.8 4.2 - - - +
177B GLU* 3.0 41.0 + - - +
265B LYS* 5.7 1.4 - - - +
268B GLN* 2.8 21.2 + - - +
269B LEU* 3.6 29.6 + - - +
271B SER* 1.3 79.1 + - - +
273B TYR* 1.3 55.2 + - - +
275B LYS* 2.8 24.8 + - - +
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Residues in contact with TYR 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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175B TRP* 3.4 31.4 - + + -
177B GLU* 4.2 20.9 - - + +
180B GLY 4.2 2.4 - - - -
181B ASP* 3.4 30.3 + - - +
182B LEU* 3.8 12.1 - - + -
269B LEU 3.1 16.9 + - - +
270B HIS* 4.1 1.6 - - - +
271B SER 3.0 0.6 - - - -
272B ARG* 1.3 79.0 - - - +
274B TYR* 1.3 102.7 + + - +
275B LYS* 3.3 12.2 + - - +
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Residues in contact with TYR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ASP* 2.4 28.6 + - - -
182B LEU* 3.5 21.4 + - + -
183B ASN* 3.0 45.0 + - - +
270B HIS* 2.7 36.2 + + - +
273B TYR* 1.3 93.2 - + - +
275B LYS* 1.3 68.6 + - - +
276B THR* 3.0 25.2 + - + +
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Residues in contact with LYS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B SER* 2.6 30.4 + - - +
272B ARG* 2.8 26.2 + - - +
273B TYR* 4.0 7.9 + - - +
274B TYR* 1.3 75.3 - - - +
276B THR* 1.3 56.6 + - - +
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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