Contacts of the helix formed by residues 254 - 272 (chain C) in PDB entry 2PCB
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 254 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C ASN* 4.8 0.2 + - - -
250C GLU* 3.1 14.0 + - + +
251C TYR 3.6 6.7 + - - +
252C ALA 3.7 0.2 - - - -
253C ASN* 1.3 77.4 - - + +
255C GLN* 1.3 68.2 + - - +
256C ASP* 3.0 27.1 + - - +
257C LYS* 2.9 30.7 + - + +
258C PHE* 3.1 9.7 + - - +
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Residues in contact with GLN 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A THR* 5.3 2.2 + - - -
2A THR* 3.3 34.6 + - + +
198C PHE 4.6 0.8 + - - -
199C THR* 4.1 5.7 - - - +
200C ASN* 2.3 65.3 + - + +
253C ASN 4.3 0.2 - - - -
254C ASP* 1.3 72.1 - - - +
256C ASP* 1.3 53.8 + - - +
258C PHE* 2.9 8.4 + - - -
259C PHE* 2.5 78.1 + - + -
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Residues in contact with ASP 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C ASP* 3.0 14.3 - - - +
255C GLN* 1.3 81.3 - - - +
257C LYS* 1.3 57.6 - - - +
259C PHE* 3.3 13.0 + - - +
260C LYS* 2.7 59.4 + - - +
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Residues in contact with LYS 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ARG* 4.1 11.9 - - - +
250C GLU* 3.0 32.9 + - + +
251C TYR* 3.4 14.4 - - + -
254C ASP* 2.9 32.3 + - + +
256C ASP* 1.3 69.0 - - - +
258C PHE* 1.4 58.4 + - - +
260C LYS* 2.7 27.2 + - + +
261C ASP* 2.3 34.6 + - - +
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Residues in contact with PHE 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ALA* 3.2 26.7 - - - -
173C GLY* 4.2 9.6 - - - -
198C PHE* 3.6 23.6 - + - -
199C THR 3.4 23.1 - - - -
200C ASN* 3.6 18.6 - - + -
203C TYR* 3.5 26.5 - + - -
251C TYR* 3.6 35.1 - + + +
254C ASP 3.1 3.2 + - - +
255C GLN* 2.9 10.9 + - - +
257C LYS* 1.4 80.7 - - - +
259C PHE* 1.3 88.1 + + - -
261C ASP* 4.4 0.6 - - - +
262C PHE* 2.9 26.6 + - + +
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Residues in contact with PHE 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C GLN 4.2 14.8 - - - -
121C GLY* 4.2 6.7 - - - -
122C PRO* 3.3 38.6 - - + +
198C PHE* 3.6 31.4 - + - -
199C THR 4.4 0.9 - - - -
255C GLN* 2.5 60.1 + - + +
256C ASP* 3.4 16.4 - - - +
257C LYS 3.1 0.2 - - - -
258C PHE* 1.3 95.5 - + - +
260C LYS* 1.3 65.8 - - + +
262C PHE* 3.8 1.7 - - - +
263C SER* 3.3 18.0 + - - -
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Residues in contact with LYS 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C ASP* 2.7 56.1 + - - +
257C LYS* 2.7 19.6 + - + +
259C PHE* 1.3 75.4 - - + +
261C ASP* 1.3 64.4 - - - +
263C SER* 3.5 10.2 + - - -
264C LYS* 3.2 32.2 - - - +
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Residues in contact with ASP 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ARG* 3.1 23.0 + - + -
167C GLU* 6.4 0.7 - - - -
170C ALA* 4.2 6.7 - - + -
251C TYR* 2.6 34.3 + - + +
257C LYS* 2.3 49.7 + - - +
258C PHE 4.4 0.2 - - - +
260C LYS* 1.3 72.0 - - - +
262C PHE* 1.3 65.4 + - - +
263C SER 3.2 0.2 - - - -
264C LYS* 3.5 17.8 + - - +
265C ALA* 3.1 25.6 + - - +
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Residues in contact with PHE 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 5.8 1.1 - - + -
116C VAL* 4.5 11.4 - - + -
122C PRO* 4.7 3.8 - - + -
124C ILE* 4.4 8.5 - - + -
170C ALA* 3.2 25.7 - - - +
171C LEU* 3.3 35.4 - - + -
174C ALA* 4.2 9.0 - - + -
198C PHE* 3.7 31.6 - + + -
258C PHE* 2.9 32.9 + + + +
259C PHE* 3.8 5.8 - - - +
260C LYS 3.3 0.2 - - - -
261C ASP* 1.3 75.5 - - - +
263C SER* 1.3 52.8 + - - +
265C ALA* 3.4 1.1 - - - +
266C PHE* 2.6 78.4 + + + +
295C HEM 4.1 8.3 - - + -
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Residues in contact with SER 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C PRO* 3.3 20.4 - - - +
123C LYS 2.7 28.5 + - - -
124C ILE* 3.6 15.5 - - - +
125C PRO* 4.8 8.7 - - - +
259C PHE 3.3 3.2 + - - -
260C LYS 3.5 11.7 - - - -
261C ASP 3.2 0.4 - - - -
262C PHE* 1.3 79.7 - - - +
264C LYS* 1.3 54.9 + - - +
266C PHE* 3.2 0.9 + - - -
267C GLU* 2.8 35.0 + - - +
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Residues in contact with LYS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLU* 5.5 2.7 - - - +
260C LYS* 3.2 36.6 + - - +
261C ASP* 3.7 16.8 + - - +
263C SER* 1.3 73.9 - - - +
265C ALA* 1.3 54.9 + - + +
267C GLU* 3.2 8.4 + - - +
268C LYS* 2.7 37.0 + - - +
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Residues in contact with ALA 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C MET* 4.1 4.8 - - - +
167C GLU* 4.3 27.6 - - + +
170C ALA* 4.9 2.7 - - + -
171C LEU* 3.8 21.6 - - + +
261C ASP 3.1 18.6 - - - +
262C PHE* 3.4 4.9 - - - +
264C LYS* 1.3 74.1 - - - +
266C PHE* 1.3 59.6 - - - +
268C LYS* 3.3 7.2 + - - +
269C LEU* 2.8 36.0 + - - +
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Residues in contact with PHE 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 4.5 11.4 - - + -
50C ALA* 4.6 3.8 - - + -
51C TRP* 5.0 1.3 - - + -
112C GLY* 4.0 19.5 - - - -
113C VAL* 3.9 29.2 - - + -
116C VAL* 4.4 9.6 - - + -
124C ILE* 3.8 28.5 - - + -
171C LEU* 3.7 7.6 - - + +
262C PHE* 2.6 52.0 + + + +
263C SER 3.8 3.4 - - - +
265C ALA* 1.3 75.3 - - - +
267C GLU* 1.3 62.6 + - - +
269C LEU* 3.3 12.1 + - + +
270C LEU* 3.1 42.7 + - + +
295C HEM 3.9 23.1 - - + -
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Residues in contact with GLU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ILE* 3.9 14.9 - - + +
125C PRO* 3.4 39.7 - - + +
127C ARG* 3.9 8.3 + - - +
263C SER 2.8 16.1 + - - +
264C LYS* 3.2 7.0 + - - +
266C PHE* 1.3 75.8 - - - +
268C LYS* 1.3 66.5 + - - +
270C LEU* 2.8 9.5 + - + +
271C GLU* 2.4 61.5 + - - +
283C PRO* 4.1 5.6 - - - +
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Residues in contact with LYS 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C LEU 3.7 3.2 + - - -
162C ASN* 2.9 37.0 + - - +
163C MET* 3.5 19.2 - - + +
167C GLU* 3.1 34.1 - - - +
264C LYS 2.7 19.4 + - - +
265C ALA* 3.6 2.9 - - - +
267C GLU* 1.3 73.7 - - - +
269C LEU* 1.3 55.3 + - - +
271C GLU* 3.5 6.5 - - - +
272C ASN* 2.8 52.9 + - - +
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TRP* 3.6 50.0 - - + -
54C SER* 3.7 26.8 - - - +
55C GLY* 4.6 1.8 - - - +
66C SER 5.9 0.2 + - - -
158C PHE* 5.9 0.2 - - + -
161C LEU* 4.4 11.4 - - + -
163C MET* 3.7 19.1 - - + -
171C LEU* 4.3 16.6 - - + -
265C ALA 2.8 18.7 + - - +
266C PHE* 3.3 20.0 - - + +
268C LYS* 1.3 79.5 - - - +
270C LEU* 1.3 61.7 + - + +
272C ASN* 3.7 17.5 + - - +
295C HEM 5.2 0.7 - - + -
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ALA* 4.2 20.6 - - + +
54C SER* 3.3 22.4 - - - +
66C SER* 2.5 27.5 + - - -
109C SER* 3.7 37.0 - - - +
113C VAL* 3.7 20.4 - - + -
124C ILE* 5.6 0.2 - - + -
126C TRP* 4.7 5.8 - - + -
130C ARG* 3.6 16.0 + - - +
266C PHE* 3.1 34.3 + - + +
267C GLU* 2.8 14.1 + - + +
269C LEU* 1.3 76.6 - - + +
271C GLU* 1.3 61.3 + - + +
272C ASN 3.5 0.4 + - - -
274C ILE* 3.9 0.2 - - - +
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Residues in contact with GLU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C TRP* 4.6 1.2 - - - -
127C ARG* 2.6 41.3 + - - +
130C ARG* 4.3 8.9 + - - +
267C GLU* 2.4 55.4 + - + +
268C LYS* 3.5 5.0 + - - +
270C LEU* 1.3 80.8 - - + +
272C ASN* 1.3 67.5 + - - +
273C GLY 3.1 1.9 + - - -
274C ILE* 3.0 25.1 + - - +
276C PHE* 3.8 20.2 - - + -
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Residues in contact with ASN 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C SER 5.7 0.4 - - - +
57C TRP* 3.2 48.4 + - + -
65C GLY* 4.7 9.8 - - - -
66C SER 4.7 1.0 + - - -
67C TYR* 5.6 0.9 + - - +
161C LEU* 3.3 19.8 + - - +
162C ASN* 5.0 1.0 + - - -
163C MET* 3.7 17.2 - - - +
268C LYS* 2.8 31.7 + - - +
269C LEU* 3.8 18.0 + - - +
270C LEU 3.5 3.3 - - - +
271C GLU* 1.3 77.5 - - - +
273C GLY* 1.3 60.0 + - - +
274C ILE* 3.7 7.1 + - - +
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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
------------------------------------------------------------
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