Contacts of the helix formed by residues 250 - 258 (chain B) in PDB entry 4NAW
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 PRO 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B LEU* 4.2 29.8 - - + +
213B HIS 3.6 10.1 - - - +
214B THR* 4.2 3.4 - - + -
248B GLU 3.3 9.2 - - - +
249B THR* 1.3 83.4 - - + +
251B LEU* 1.3 64.9 + - - +
252B GLN 3.4 0.7 - - - +
253B TRP* 3.3 14.0 + - + +
254B LEU* 3.2 20.4 + - - +
13C TRP* 3.5 38.8 - - + +
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Residues in contact with LEU 251 (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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185B ILE* 3.7 26.7 - - + -
203B PHE* 3.5 38.4 - - + -
205B PRO* 4.9 3.4 - - + -
213B HIS* 2.9 20.0 + - + +
214B THR 4.2 6.3 - - - -
215B LEU* 4.7 7.0 - - + -
218B LEU* 3.8 31.4 - - + -
249B THR 3.4 4.2 + - - -
250B PRO* 1.3 69.0 - - - +
252B GLN* 1.3 66.9 + - - +
254B LEU* 3.1 14.9 + - + +
255B SER* 2.9 22.9 + - - -
265B LEU* 3.9 21.5 - - + -
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Residues in contact with GLN 252 (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 TYR* 3.8 8.0 - - + +
180B ASN 4.3 5.6 - - - +
181B GLY* 3.4 16.4 - - - -
182B PHE* 3.0 51.5 + - - +
185B ILE* 3.6 10.8 - - - +
205B PRO* 3.4 22.0 - - + +
212B LEU* 4.5 21.3 - - + -
213B HIS 4.6 1.2 + - - -
250B PRO* 3.4 0.6 - - - +
251B LEU* 1.3 77.6 - - - +
253B TRP* 1.3 63.2 + - - +
255B SER* 3.3 2.9 + - - -
256B GLU* 2.8 55.9 + - - +
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Residues in contact with TRP 253 (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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4B ASP* 3.2 29.9 + - - -
7B VAL* 4.1 22.4 - - + -
212B LEU* 6.0 0.6 - - + +
249B THR* 4.3 2.5 - - + -
250B PRO* 3.3 17.0 + - + +
251B LEU 3.2 0.4 - - - -
252B GLN* 1.3 79.2 - - - +
254B LEU* 1.3 73.3 + - + +
256B GLU* 3.2 7.2 + - - -
257B HIS* 2.7 71.0 + + + -
258B LEU* 4.2 9.2 - - + -
13C TRP* 3.6 31.9 - + + -
14C LYS* 3.7 21.9 - - + +
17C ILE* 3.7 32.3 - - + -
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Residues in contact with LEU 254 (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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215B LEU* 4.0 37.2 - - + -
240B ILE* 4.7 8.3 - - + -
245B PRO* 4.7 6.1 - - + -
249B THR* 3.6 32.3 - - + +
250B PRO 3.2 7.7 + - - +
251B LEU* 3.1 15.3 + - + +
253B TRP* 1.3 84.9 - - + +
255B SER* 1.3 58.4 + - - +
258B LEU* 2.7 64.8 + - + +
259B SER 3.4 2.3 + - - -
265B LEU* 3.8 13.6 - - + +
17C ILE* 4.2 9.2 - - + -
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Residues in contact with SER 255 (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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136B LYS* 4.7 1.0 - - - +
173B MET* 3.7 8.1 - - - +
182B PHE* 3.4 20.9 - - - -
185B ILE* 3.8 31.4 - - - +
186B PRO* 4.0 9.2 + - - +
251B LEU 2.9 15.7 + - - -
252B GLN 3.6 5.6 - - - -
254B LEU* 1.3 76.4 - - - +
256B GLU* 1.3 61.9 + - - +
259B SER* 2.6 33.2 + - - -
263B ASN 5.1 0.7 + - - -
265B LEU* 3.8 6.4 - - - +
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Residues in contact with GLU 256 (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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8B LEU* 4.0 1.7 - - - +
166B TRP* 3.7 23.9 - - - -
173B MET* 3.9 26.9 - - + +
175B TYR* 3.6 16.6 + - - -
182B PHE* 4.1 11.2 - - + -
252B GLN* 2.8 47.7 + - - +
253B TRP* 3.5 5.4 - - - +
254B LEU 3.1 0.2 - - - -
255B SER* 1.3 78.4 - - - +
257B HIS* 1.3 87.3 + - + +
259B SER* 4.9 0.7 + - - -
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Residues in contact with HIS 257 (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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4B ASP* 3.5 40.1 + - + +
7B VAL* 4.1 5.3 - - + +
8B LEU* 3.6 34.7 - - + +
11B VAL* 3.7 14.0 - - - +
166B TRP* 5.8 0.6 - - - -
253B TRP* 2.7 68.6 + + + +
256B GLU* 1.3 107.3 - - + +
258B LEU* 1.3 65.4 + - - +
259B SER 3.6 2.9 - - - +
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Residues in contact with LEU 258 (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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7B VAL* 3.6 24.2 - - + -
11B VAL* 3.9 9.0 - - + -
240B ILE* 4.1 22.4 - - + +
241B HIS* 2.9 34.2 + - + -
243B ILE* 4.1 24.9 - - + -
245B PRO* 4.7 2.9 - - + -
253B TRP* 4.2 14.1 - - + -
254B LEU* 2.7 42.5 + - + +
257B HIS* 1.3 79.5 - - - +
259B SER* 1.3 60.0 + - - +
260B TYR* 3.8 1.6 + - - -
265B LEU* 3.6 14.0 - - + +
17C ILE* 4.3 8.1 - - + -
21C LEU* 4.8 1.6 - - + -
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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