Contacts of the helix formed by residues 256 - 275 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A SER 4.3 1.1 - - - +
123A PHE 3.0 11.2 + - - +
124A THR 3.6 21.6 - - - +
125A LYS* 3.6 21.6 - - - +
126A THR* 4.6 0.9 + - - -
166A ASP* 4.8 1.2 - - - +
255A VAL* 1.3 70.3 - - - +
257A GLU* 1.3 60.9 + - - +
258A GLU* 3.2 12.5 + - - +
259A ARG* 2.9 55.5 + - + +
260A LEU* 3.2 24.6 + - - +
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Residues in contact with GLU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 3.5 9.9 + - + +
256A ASP* 1.3 70.6 + - - +
258A GLU* 1.3 61.9 + - + +
260A LEU* 3.3 5.8 + - - +
261A GLY* 2.9 26.2 + - - -
293A VAL* 3.8 28.9 - - + +
297A LEU* 3.5 38.5 + - + +
300A PRO* 5.4 5.7 - - - +
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Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS* 4.8 11.2 + - - -
256A ASP* 3.2 8.6 + - - +
257A GLU* 1.3 75.3 - - + +
259A ARG* 1.3 68.4 + - - +
261A GLY* 3.0 11.9 + - - -
262A LEU* 3.0 19.5 + - + +
154B LYS* 6.1 1.4 - - - +
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Residues in contact with ARG 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL 5.8 0.4 - - - -
121A PHE 4.3 0.6 + - - -
122A SER* 2.8 49.4 + - - +
124A THR 2.8 27.9 + - - -
126A THR* 3.0 27.9 + - - +
162A TYR* 4.6 10.9 + - - -
165A PHE* 4.4 7.4 - - - -
166A ASP* 2.9 38.1 + - - +
169A LEU* 4.0 13.2 - - + -
256A ASP* 2.9 42.5 + - - +
258A GLU* 1.3 75.7 - - - +
260A LEU* 1.3 59.0 + - - +
262A LEU* 3.0 13.8 + - + +
263A PHE* 2.8 40.7 + - + +
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER 4.2 3.4 - - - +
123A PHE* 4.0 14.4 - - + -
255A VAL* 4.3 2.9 - - + -
256A ASP 3.2 18.1 + - - +
257A GLU* 3.9 5.8 - - - +
258A GLU 3.1 0.8 - - - -
259A ARG* 1.3 76.2 - - - +
261A GLY* 1.3 61.0 + - - +
263A PHE* 3.3 16.0 + - + +
264A SER* 3.1 26.0 + - - -
286A LEU* 3.5 28.7 - - + -
289A VAL* 3.6 31.6 - - + -
290A SER* 3.7 22.4 + - - +
293A VAL* 3.7 23.1 - - + -
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Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU 2.9 15.1 + - - -
258A GLU* 3.0 4.2 + - - -
260A LEU* 1.3 76.9 - - - +
262A LEU* 1.3 56.7 + - - +
264A SER* 3.0 21.2 + - - -
265A LYS* 3.1 31.5 + - - -
293A VAL* 6.2 0.2 - - - +
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASP* 4.5 8.7 - - + +
169A LEU* 3.4 31.9 - - + -
170A LYS* 3.7 38.1 - - + +
173A ILE* 3.7 28.7 - - + +
258A GLU* 3.0 18.4 + - + +
259A ARG* 3.3 11.4 - - + +
261A GLY* 1.3 75.7 - - - +
263A PHE* 1.3 61.8 + - - +
265A LYS* 3.6 15.6 + - - +
266A TYR* 3.1 26.2 + - - +
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Residues in contact with PHE 263 (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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122A SER* 3.4 37.0 - - - -
165A PHE* 4.3 15.7 - + - -
169A LEU* 3.9 21.3 - - + -
259A ARG* 2.8 31.2 + - + -
260A LEU* 3.5 29.6 - - + +
261A GLY 3.3 0.2 - - - -
262A LEU* 1.3 72.3 - - - +
264A SER* 1.3 58.3 + - - +
266A TYR* 4.6 0.2 - - - -
267A SER* 2.9 17.5 + - - -
280A TYR* 2.8 62.8 + + + +
286A LEU* 3.9 15.5 - - + -
290A SER* 5.6 2.7 - - - +
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Residues in contact with SER 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU 3.1 11.6 + - - -
261A GLY* 3.0 12.2 + - - -
263A PHE* 1.3 75.4 - - - +
265A LYS* 1.3 68.4 + - - +
266A TYR 3.1 1.3 - - - -
267A SER* 3.0 6.4 + - - -
268A GLN* 2.9 35.9 + - - +
290A SER* 5.4 4.7 + - - -
294A GLN* 4.4 16.1 + - - -
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Residues in contact with LYS 265 (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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173A ILE* 4.1 25.7 - - + +
261A GLY* 3.1 24.0 + - - +
262A LEU* 4.1 19.7 - - - +
264A SER* 1.3 79.6 - - - +
266A TYR* 1.3 64.4 + - - +
268A GLN* 3.1 17.5 + - - +
269A LEU* 3.1 24.8 + - + +
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Residues in contact with TYR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 4.1 11.2 - - + -
172A ASN* 3.4 45.5 + - + -
173A ILE* 3.4 17.0 - - + +
182A LEU* 4.4 6.7 - - + -
183A ASN* 5.4 0.5 + - - -
186A VAL* 3.2 26.0 - - + +
262A LEU 3.1 17.0 + - - +
265A LYS* 1.3 80.8 - - - +
267A SER* 1.3 61.8 + - - +
269A LEU* 3.3 11.5 + - + +
270A HIS* 2.8 58.6 + + - -
278A PRO* 4.2 4.7 - - + -
280A TYR* 3.2 36.6 - + - +
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Residues in contact with SER 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PHE 2.9 23.1 + - - -
264A SER* 3.0 7.6 + - - -
266A TYR* 1.3 78.0 - - - +
268A GLN* 1.3 62.0 + - - +
270A HIS* 3.1 13.5 + - - +
271A SER* 3.2 12.0 + - - -
277A LEU* 3.9 19.2 - - - +
278A PRO* 3.7 10.8 - - - +
280A TYR* 3.0 12.3 + - - -
281A ASN* 3.6 21.2 + - - -
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Residues in contact with GLN 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A SER* 2.9 32.2 + - - +
265A LYS* 3.1 17.3 + - - +
267A SER* 1.3 75.0 - - - +
269A LEU* 1.3 66.0 + - + +
271A SER* 3.2 9.7 + - - +
272A ARG* 3.0 40.3 + - + +
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Residues in contact with LEU 269 (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 ASN 4.2 6.1 - - - +
173A ILE* 3.8 41.3 - - + +
175A TRP* 4.2 31.5 - - + +
182A LEU* 4.0 8.0 - - + +
265A LYS* 3.1 17.1 + - + +
266A TYR* 3.5 13.2 - - + +
267A SER 3.3 0.2 - - - -
268A GLN* 1.3 75.4 - - - +
270A HIS* 1.3 63.5 + - + +
272A ARG* 3.4 38.3 + - - +
273A TYR* 3.2 25.3 + - - +
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Residues in contact with HIS 270 (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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182A LEU* 3.1 31.1 - - + +
183A ASN* 3.6 24.7 - - - -
266A TYR* 2.8 52.4 + + - -
267A SER 3.1 9.8 + - - +
269A LEU* 1.3 79.2 - - - +
271A SER* 1.3 54.7 + - - +
274A TYR* 2.6 47.7 + + + +
276A THR* 3.2 18.1 - - - +
277A LEU 4.9 1.4 - - - -
278A PRO* 3.7 28.0 - - + +
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Residues in contact with SER 271 (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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267A SER 3.2 11.9 + - - -
268A GLN* 3.2 16.3 + - - -
270A HIS* 1.3 72.8 - - - +
272A ARG* 1.3 63.8 + - - +
275A LYS* 2.7 31.8 + - - +
276A THR 3.2 20.2 + - - +
277A LEU* 4.4 11.4 - - - +
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Residues in contact with ARG 272 (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 TRP* 4.6 2.4 - - - -
177A GLU* 3.6 30.6 + - - +
268A GLN* 3.0 25.9 + - + +
269A LEU* 3.4 39.3 + - - +
271A SER* 1.3 77.1 + - - +
273A TYR* 1.3 57.6 + - - +
275A LYS* 2.9 31.8 + - - +
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Residues in contact with TYR 273 (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 TRP* 3.3 34.3 - + + -
177A GLU* 4.1 21.5 + - + +
180A GLY 3.7 5.9 + - - -
181A ASP* 3.6 35.1 + - - +
182A LEU* 3.7 13.5 - - + -
269A LEU 3.2 16.5 + - - +
270A HIS 4.0 1.1 - - - +
272A ARG* 1.3 81.0 - - - +
274A TYR* 1.3 90.5 + + + +
275A LYS* 3.5 7.0 + - - +
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Residues in contact with TYR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ASP* 2.3 31.9 + - - -
182A LEU* 3.4 20.9 + - + -
183A ASN* 2.9 48.3 + - - -
270A HIS* 2.6 31.5 + - - +
273A TYR* 1.3 97.9 - + - +
275A LYS* 1.3 70.9 + - - +
276A THR* 2.8 26.1 + - + +
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Residues in contact with LYS 275 (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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271A SER* 2.7 24.7 + - - +
272A ARG* 2.9 24.4 + - - +
273A TYR 4.3 6.3 + - - +
274A TYR* 1.3 82.7 - - - +
276A THR* 1.3 57.2 + - - +
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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
------------------------------------------------------------
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