Contacts of the helix formed by residues 254 - 272 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A GLU 3.3 13.7 + - - +
251A TYR* 3.4 10.1 + - - +
253A ASN* 1.3 85.7 - - - +
255A GLN* 1.3 59.1 + - - +
256A ASP* 3.1 9.7 + - - +
257A LYS* 2.5 43.7 + - + +
258A PHE* 3.2 17.0 + - - +
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Residues in contact with GLN 255 (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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198A PHE 3.8 1.0 + - - -
199A THR* 3.7 22.2 - - - +
200A ASN* 3.6 36.2 + - + +
253A ASN 4.2 0.4 - - - -
254A ASP* 1.3 69.0 - - - +
256A ASP* 1.3 61.5 + - - +
257A LYS 2.9 1.8 - - - -
258A PHE* 2.9 6.0 + - + +
259A PHE* 2.7 82.1 + - + +
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Residues in contact with ASP 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASP* 3.1 9.2 + - - +
255A GLN* 1.3 80.5 - - - +
257A LYS* 1.3 56.4 + - - +
259A PHE* 3.6 19.4 - - - +
260A LYS* 3.0 33.1 + - - +
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Residues in contact with LYS 257 (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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166A ARG* 3.2 26.3 - - - +
250A GLU* 3.8 12.3 - - + +
251A TYR* 3.6 15.3 - - + -
254A ASP* 2.5 29.8 + - + +
256A ASP* 1.3 72.1 - - - +
258A PHE* 1.3 70.1 + - - +
260A LYS* 2.5 32.1 + - + +
261A ASP* 2.7 40.2 + - - +
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Residues in contact with PHE 258 (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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170A ALA* 3.3 16.8 - - - -
173A GLY* 3.9 20.9 - - - -
198A PHE* 3.7 31.2 - + - -
199A THR 3.5 19.1 - - - -
200A ASN* 4.0 14.4 - - + -
203A TYR* 3.1 36.3 - + - -
251A TYR* 3.7 33.0 - + + -
254A ASP 3.2 7.0 + - - +
255A GLN* 2.9 9.6 + - - +
257A LYS* 1.3 81.9 - - - +
259A PHE* 1.3 83.6 + + - +
261A ASP* 3.1 3.5 + - - +
262A PHE* 2.9 23.7 + + + +
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Residues in contact with PHE 259 (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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120A GLN 4.0 11.4 - - - -
121A GLY 4.4 0.9 - - - -
122A PRO* 3.7 42.1 - - + +
198A PHE* 3.3 31.9 - + - -
199A THR* 4.2 0.7 - - - -
255A GLN* 2.7 54.9 + - + +
256A ASP* 3.6 21.3 - - - +
258A PHE* 1.3 94.2 - + - +
260A LYS* 1.4 61.5 + - - +
262A PHE* 4.5 2.5 - - - -
263A SER* 3.0 29.3 + - - -
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Residues in contact with LYS 260 (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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256A ASP* 3.0 20.7 + - - +
257A LYS* 2.5 27.8 + - - +
259A PHE* 1.4 73.9 - - - +
261A ASP* 1.3 72.7 + - - +
263A SER* 3.6 10.0 + - - -
264A LYS* 3.6 23.9 + - + +
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Residues in contact with ASP 261 (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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166A ARG* 2.9 31.5 + - + +
170A ALA* 3.8 8.3 - - + +
251A TYR* 2.4 31.3 + - + +
257A LYS* 2.7 35.7 + - - +
258A PHE 3.6 6.7 - - - +
260A LYS* 1.3 79.2 - - - +
262A PHE* 1.3 61.6 + - - +
264A LYS* 3.4 11.5 - - - +
265A ALA* 3.1 25.6 + - - +
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Residues in contact with PHE 262 (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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47A VAL* 4.8 4.7 - - + -
116A VAL* 4.0 12.6 - - + -
122A PRO* 4.6 2.0 - - + -
124A ILE* 3.9 7.6 - - + -
170A ALA* 3.2 28.2 - - - +
171A LEU* 3.9 12.3 - - + -
174A ALA* 3.9 28.3 - - + -
198A PHE* 3.9 33.4 - + + -
258A PHE* 2.9 22.2 + + + +
259A PHE* 3.4 7.4 + - - +
260A LYS 3.3 0.2 - - - -
261A ASP* 1.3 72.8 - - - +
263A SER* 1.3 71.5 + - - +
264A LYS 3.0 1.3 - - - -
265A ALA* 3.1 1.7 + - - -
266A PHE* 2.7 72.0 + + + +
295A HEM 4.6 2.5 - - + -
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Residues in contact with SER 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 PRO* 3.6 11.1 - - - +
123A LYS 3.3 27.1 + - - -
124A ILE* 3.4 19.9 - - - +
125A PRO* 4.5 7.7 - - - +
259A PHE 3.0 16.4 + - - -
260A LYS* 4.0 3.6 + - - -
262A PHE* 1.3 80.9 - - - +
264A LYS* 1.3 65.9 + - - +
267A GLU* 3.1 26.0 + - - +
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Residues in contact with LYS 264 (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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260A LYS* 3.6 22.1 + - + +
261A ASP* 3.4 16.8 - - - +
263A SER* 1.3 79.2 - - - +
265A ALA* 1.3 56.8 + - + +
267A GLU* 3.9 4.9 - - - +
268A LYS* 2.9 28.3 + - - +
35C GLU* 2.5 46.7 + - - +
39C TYR* 3.7 19.9 + - - +
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Residues in contact with ALA 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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163A MET* 4.1 21.6 - - + +
167A GLU* 4.2 20.2 - - + +
170A ALA* 5.1 1.8 - - + -
171A LEU* 3.9 18.4 - - + +
261A ASP 3.1 13.6 + - - +
262A PHE* 3.1 4.3 + - - +
264A LYS* 1.3 76.7 - - + +
266A PHE* 1.3 58.5 - - - +
268A LYS* 3.5 8.5 - - - +
269A LEU* 2.8 32.4 + - - +
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Residues in contact with PHE 266 (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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47A VAL* 4.2 10.1 - - + -
50A ALA* 3.8 24.0 - - + -
51A TRP* 4.4 2.9 - - + -
112A GLY* 4.2 9.9 - - - -
113A VAL* 4.8 1.3 - - + -
116A VAL* 4.2 18.8 - - + -
124A ILE* 4.4 16.4 - - + -
171A LEU* 3.8 10.9 - - + +
262A PHE* 2.7 44.6 + + + +
263A SER 4.2 1.6 - - - +
265A ALA* 1.3 75.4 - - - +
267A GLU* 1.3 58.9 + - - +
269A LEU* 2.9 51.7 - - + +
270A LEU* 2.9 33.1 + - + +
295A HEM 3.5 19.1 - - + -
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Residues in contact with GLU 267 (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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124A ILE* 4.0 7.9 - - + +
125A PRO* 2.8 50.8 - - - +
127A ARG* 4.0 9.2 - - - +
263A SER 3.1 18.1 + - - +
264A LYS* 4.3 3.8 - - - +
266A PHE* 1.3 74.3 - - - +
268A LYS* 1.3 62.8 + - - +
270A LEU* 3.6 8.6 - - - +
271A GLU* 2.5 71.8 + - - +
283A PRO* 4.1 6.7 - - - +
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Residues in contact with LYS 268 (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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162A ASN* 2.7 26.7 + - - -
163A MET* 2.9 21.2 - - + +
167A GLU* 2.5 38.8 + - - +
264A LYS 2.9 18.2 + - - +
265A ALA* 3.5 4.5 - - - +
266A PHE 3.1 0.2 - - - -
267A GLU* 1.3 80.8 - - - +
269A LEU* 1.4 53.5 - - - +
271A GLU* 3.1 5.5 + - - +
272A ASN* 2.8 51.8 + - - +
34C ASP* 3.4 14.6 - - - -
39C TYR* 3.4 35.9 - - + +
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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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51A TRP* 3.9 37.9 - - + -
54A SER* 3.7 24.8 - - - +
66A SER* 5.5 0.3 - - - -
158A PHE* 5.8 0.2 - - + -
161A LEU* 4.4 20.0 - - + -
163A MET* 4.9 4.5 - - - -
171A LEU* 4.0 23.1 - - + -
265A ALA 2.8 12.8 + - - +
266A PHE* 2.9 45.1 - - + +
268A LYS* 1.4 79.1 - - - +
270A LEU* 1.3 61.5 + - + -
271A GLU 3.3 0.2 + - - -
272A ASN* 3.5 19.8 + - - +
295A HEM 4.4 1.1 - - + -
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Residues in contact with LEU 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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50A ALA* 3.6 19.7 - - + +
54A SER* 3.2 24.2 - - - +
66A SER* 3.0 24.2 + - - -
109A SER* 3.8 34.5 - - - +
113A VAL* 4.4 11.9 - - + -
124A ILE* 6.0 0.4 - - + -
126A TRP* 4.9 3.4 - - + -
130A ARG* 3.4 23.7 + - - +
266A PHE* 2.9 51.9 + - + +
267A GLU* 3.2 8.0 + - - +
269A LEU* 1.3 75.3 - - + +
271A GLU* 1.3 60.1 + - - +
272A ASN 5.0 0.2 - - - -
274A ILE* 3.5 1.9 - - - +
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Residues in contact with GLU 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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125A PRO 4.6 0.2 - - - +
126A TRP* 4.3 1.7 - - - -
127A ARG* 3.4 32.6 + - - +
130A ARG* 4.1 7.1 + - - +
267A GLU* 2.5 57.8 + - - +
268A LYS* 3.5 3.9 - - - +
270A LEU* 1.3 81.7 - - - +
272A ASN* 1.3 68.8 + - - +
273A GLY 3.1 2.1 + - - -
274A ILE* 3.2 20.4 + - - +
276A PHE* 3.2 27.3 - - + -
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Residues in contact with ASN 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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54A SER 5.9 0.6 + - - +
57A TRP* 3.5 44.0 + - + +
65A GLY* 5.1 1.2 - - - -
66A SER* 4.7 7.6 + - - -
161A LEU* 3.6 27.2 + - - +
162A ASN* 5.0 2.9 - - - +
163A MET* 4.5 5.3 - - - -
268A LYS* 2.8 39.8 + - - +
269A LEU* 3.5 20.5 + - - +
270A LEU 4.6 0.5 - - - +
271A GLU* 1.3 73.6 - - - +
273A GLY* 1.3 57.7 + - - +
274A ILE* 3.5 12.0 + - - +
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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