Contacts of the helix formed by residues 261 - 278 (chain E) in PDB entry 1PF7
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 LEU 261 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E GLU* 2.8 35.2 + - + +
259E GLU* 3.9 12.1 - - + -
260E VAL* 1.3 78.7 - - - +
262E ALA* 1.3 77.7 + - + +
264E GLY* 2.8 16.6 + - - -
265E LYS* 2.7 49.0 + - + +
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Residues in contact with ALA 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E VAL* 5.8 5.4 - - + -
127E GLY* 6.5 0.2 - - - -
240E LEU* 5.8 0.7 - - - -
259E GLU* 3.0 16.7 + - + +
261E LEU* 1.3 88.3 - - + +
263E ALA* 1.3 51.8 + - - +
264E GLY 3.0 6.1 - - - -
265E LYS* 2.7 44.9 + - + +
267E ALA* 4.2 10.9 + - + +
268E ALA* 3.8 8.1 + - - +
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Residues in contact with ALA 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E SER* 4.1 6.3 - - - +
34E GLY* 2.6 50.1 - - - +
240E LEU* 4.9 7.9 - - + -
242E THR* 5.5 5.8 - - + -
259E GLU 3.3 3.9 + - - +
260E VAL* 2.9 34.2 - - + +
262E ALA* 1.3 75.6 - - - +
264E GLY* 1.3 55.8 + - - +
265E LYS 3.2 2.5 - - - -
268E ALA* 3.1 12.7 - - - +
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Residues in contact with GLY 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E VAL 3.1 4.1 + - - -
261E LEU 2.8 8.8 + - - -
263E ALA* 1.3 77.7 - - - +
265E LYS* 1.3 71.1 + - - +
268E ALA* 5.1 0.2 - - - -
269E GLN* 4.5 5.1 - - - +
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Residues in contact with LYS 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E LEU* 2.7 48.8 + - + +
262E ALA* 2.7 28.1 + - + +
263E ALA 3.2 0.4 - - - -
264E GLY* 1.3 86.7 + - - +
266E GLN* 1.3 63.7 + - + +
267E ALA 4.6 0.4 - - - +
268E ALA* 3.3 5.4 + - - +
269E GLN* 2.9 37.7 + - - +
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Residues in contact with GLN 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E LYS* 1.3 77.4 - - + +
267E ALA* 1.3 55.2 + - - +
269E GLN* 3.3 21.0 + - - +
270E LYS* 2.7 34.8 + - - +
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Residues in contact with ALA 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E GLY* 3.7 35.4 - - - +
129E ILE* 4.4 1.7 - - - +
240E LEU* 4.0 14.2 - - + +
262E ALA* 4.2 14.0 + - + +
265E LYS* 3.4 1.2 - - - +
266E GLN* 1.3 73.4 - - - +
268E ALA* 1.3 67.2 - - - +
270E LYS* 3.2 7.8 + - - +
271E LEU* 3.0 22.0 + - - +
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Residues in contact with ALA 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLY 3.2 15.0 - - - +
35E LEU* 4.0 3.4 - - + -
240E LEU* 3.7 14.9 - - + +
262E ALA 3.8 1.2 + - - -
263E ALA* 3.1 37.7 - - - +
265E LYS 3.3 8.7 + - - +
267E ALA* 1.3 77.1 - - - +
269E GLN* 1.3 66.7 + - + +
271E LEU* 2.9 15.1 + - - +
272E GLU* 2.9 21.6 + - - +
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Residues in contact with GLN 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LYS* 4.8 4.0 + - - +
264E GLY 4.5 3.9 - - - +
265E LYS* 2.9 38.6 + - - +
266E GLN* 3.3 22.6 + - - +
268E ALA* 1.3 75.9 - - + +
270E LYS* 1.3 57.3 + - - +
272E GLU* 3.1 18.1 + - - +
273E GLN* 2.9 29.4 + - - +
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Residues in contact with LYS 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ILE* 4.2 5.8 - - + -
178E TRP* 3.9 29.8 - - + -
181E MET* 3.7 4.9 - - + +
183E GLU* 2.6 33.4 + - - +
266E GLN 2.7 19.7 + - - +
267E ALA* 3.6 7.9 - - - +
268E ALA 3.2 0.2 - - - -
269E GLN* 1.3 69.7 - - - +
271E LEU* 1.3 61.1 + - - +
273E GLN* 2.8 37.6 + - - +
274E PHE* 2.9 25.6 + - - +
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Residues in contact with LEU 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU* 3.6 35.2 - - + -
114E THR* 4.5 5.6 - - + -
129E ILE* 3.4 29.5 - - + +
238E PHE* 3.6 31.0 - - + -
240E LEU* 3.9 21.1 - - + +
267E ALA 3.0 9.3 + - - +
268E ALA* 2.9 10.1 + - - +
270E LYS* 1.3 75.8 - - - +
272E GLU* 1.3 58.0 + - - +
274E PHE* 3.2 5.2 + - + -
275E VAL* 2.8 48.4 + - + +
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Residues in contact with GLU 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLY 3.3 23.2 - - - +
35E LEU* 3.6 17.3 - - + +
37E GLY* 3.5 16.0 + - - +
38E LEU* 3.6 42.3 - - + +
41E LYS* 3.2 25.3 + - - +
268E ALA* 2.9 22.2 + - - +
269E GLN* 3.3 13.3 + - - +
271E LEU* 1.3 77.2 - - - +
273E GLN* 1.3 56.6 + - - +
275E VAL* 3.6 0.3 + - - +
276E SER* 3.0 27.5 + - - -
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Residues in contact with GLN 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LYS* 4.2 9.2 - - - +
181E MET* 3.4 13.2 - - - +
269E GLN 2.9 14.3 + - - +
270E LYS* 2.8 43.0 + - - +
272E GLU* 1.3 75.2 - - - +
274E PHE* 1.3 66.3 + - - +
276E SER* 3.1 6.8 + - - -
277E ILE* 2.8 41.0 + - + +
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Residues in contact with PHE 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ILE* 4.7 2.0 - - + -
174E ALA* 3.1 30.1 - - - -
177E THR* 3.6 21.1 - - + -
178E TRP* 3.7 26.0 - + + -
181E MET* 3.4 18.8 - - - -
187E LEU* 3.6 22.4 - - + -
238E PHE* 3.5 31.2 - + - -
270E LYS 2.9 17.9 + - - +
271E LEU* 3.5 12.1 - - + +
273E GLN* 1.3 77.2 - - - +
275E VAL* 1.3 57.0 + - - +
277E ILE* 3.1 8.7 + - - +
278E LEU* 2.9 48.8 + - + +
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Residues in contact with VAL 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ILE* 4.3 8.5 - - + -
38E LEU* 3.7 24.9 - - + -
112E VAL* 4.1 18.4 - - + -
114E THR* 4.1 12.8 - - + -
236E PHE* 6.2 0.2 - - + -
238E PHE* 4.0 17.0 - - + -
271E LEU* 2.8 40.4 + - + +
272E GLU 3.8 4.0 - - - +
274E PHE* 1.3 77.3 - - - +
276E SER* 1.3 62.3 + - - +
278E LEU* 3.2 18.7 + - - +
279E MET* 3.4 25.6 - - + +
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Residues in contact with SER 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LYS* 4.2 10.0 - - - +
73E LEU* 3.1 38.2 - - - +
74E ASN* 2.9 30.6 + - - +
272E GLU 3.0 18.9 + - - -
273E GLN* 3.4 6.7 - - - -
275E VAL* 1.3 74.7 - - - +
277E ILE* 1.3 66.3 + - - +
279E MET* 3.1 7.1 + - - +
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Residues in contact with ILE 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ASN* 3.3 11.2 + - - +
177E THR* 3.4 26.2 - - + +
180E GLN* 5.2 7.0 - - - +
181E MET* 3.6 26.5 - - + -
273E GLN* 2.8 52.7 + - + +
274E PHE* 3.5 4.9 - - - +
276E SER* 1.3 72.3 - - - +
278E LEU* 1.3 58.3 + - - +
279E MET 3.0 5.6 + - - -
280E ALA* 3.2 18.3 + - + +
281E SER* 4.4 1.4 + - - -
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Residues in contact with LEU 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E MET* 4.3 4.6 - - + +
174E ALA* 3.3 24.0 - - + +
177E THR* 3.3 26.5 - - - +
236E PHE* 4.1 13.0 - - + -
238E PHE* 3.4 39.9 - - + -
274E PHE* 2.9 35.5 + - + +
275E VAL* 3.4 10.8 - - - +
276E SER 3.2 0.6 - - - -
277E ILE* 1.3 73.4 - - - +
279E MET* 1.3 64.9 + - - +
280E ALA 3.1 0.7 - - - -
281E SER* 3.1 27.1 + - - +
282E ILE* 3.5 11.3 + - - +
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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