Contacts of the helix formed by residues 263 - 276 (chain B) in PDB entry 3H44
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 SER 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B SER* 4.0 6.1 - - - -
261B ARG 3.4 1.8 + - - -
262B GLU* 1.3 78.1 - - - +
264B LEU* 1.3 65.2 + - - +
265B ASP* 3.6 7.3 + - - +
266B ASP* 3.2 28.3 + - - +
267B LEU* 3.0 17.2 + - - +
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Residues in contact with LEU 264 (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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63B GLU* 3.5 35.9 - - + +
64B TYR 3.7 11.0 - - - +
65B ARG* 2.8 60.7 + - + +
77B LEU* 3.8 23.6 - - + +
79B SER* 4.2 12.7 + - - -
263B SER* 1.3 73.8 - - - +
265B ASP* 1.3 51.1 + - - +
267B LEU* 3.5 7.0 + - + +
268B THR* 2.6 37.1 + - - -
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Residues in contact with ASP 265 (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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65B ARG* 3.0 25.3 + - - -
263B SER* 3.2 6.8 + - - +
264B LEU* 1.3 74.1 - - - +
266B ASP* 1.3 67.2 + - - +
268B THR* 3.1 8.9 + - - -
269B ASN* 3.1 29.0 + - - +
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Residues in contact with ASP 266 (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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262B GLU* 3.8 22.9 - - + +
263B SER* 3.2 24.2 + - - +
265B ASP* 1.3 77.4 - - - +
267B LEU* 1.3 63.2 + - - +
269B ASN* 3.0 17.0 + - - +
270B LEU* 3.0 24.6 + - - +
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Residues in contact with LEU 267 (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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77B LEU* 4.0 18.6 - - + -
78B ILE 3.3 40.8 - - - +
79B SER* 4.1 4.3 - - - +
158B LEU* 4.4 9.6 - - + -
258B VAL* 4.4 12.8 - - + +
260B GLY* 4.2 12.1 - - - +
262B GLU* 3.4 48.0 - - + +
263B SER 3.0 10.9 + - - +
264B LEU* 3.8 7.0 - - - +
266B ASP* 1.3 76.0 - - - +
268B THR* 1.3 63.4 + - - +
270B LEU* 3.5 9.7 + - + +
271B VAL* 3.1 28.2 + - - +
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Residues in contact with THR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.9 26.9 - - + -
50B ILE* 6.2 2.9 - - + -
65B ARG* 2.8 19.6 + - - +
67B LEU* 4.8 12.3 - - + -
77B LEU* 3.4 15.2 - - + +
264B LEU 2.6 21.8 + - - -
265B ASP* 3.1 9.8 + - - -
267B LEU* 1.3 78.3 - - - +
269B ASN* 1.3 67.3 + - - +
271B VAL* 3.4 4.3 + - + +
272B VAL* 3.1 23.2 + - + +
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Residues in contact with ASN 269 (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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265B ASP* 3.1 16.4 + - - +
266B ASP* 3.0 18.9 + - - +
268B THR* 1.3 79.9 - - - +
270B LEU* 1.3 55.5 + - - +
272B VAL* 3.2 5.8 + - - +
273B LYS* 2.7 37.6 + - + +
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Residues in contact with LEU 270 (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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158B LEU* 4.2 32.3 - - + -
159B GLU* 3.3 49.4 - - + +
162B LEU* 4.2 12.0 - - + +
258B VAL* 5.8 1.3 - - + -
262B GLU* 5.3 9.6 - - + +
266B ASP 3.0 15.1 + - - +
267B LEU* 3.7 13.5 - - + +
268B THR 3.4 0.2 - - - -
269B ASN* 1.3 75.7 - - - +
271B VAL* 1.3 62.9 - - + +
273B LYS* 3.8 9.4 + - - +
274B LEU* 3.4 34.1 + - + +
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Residues in contact with VAL 271 (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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67B LEU* 5.5 2.7 - - + -
69B LEU* 4.1 17.3 - - + -
73B ILE* 6.0 0.2 - - + -
75B VAL* 4.2 20.4 - - + -
77B LEU* 3.6 22.2 - - + -
162B LEU* 5.2 2.0 - - + -
256B VAL* 5.0 2.2 - - + -
258B VAL* 4.0 22.7 - - + -
267B LEU 3.1 17.8 + - - +
268B THR* 3.8 4.3 - - - +
270B LEU* 1.3 73.1 - - + +
272B VAL* 1.3 54.7 + - + +
274B LEU 2.8 6.8 + - - -
275B PHE* 2.7 62.7 + - + -
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Residues in contact with VAL 272 (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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44B ASN* 3.9 19.7 - - - +
46B ALA* 4.1 7.2 - - + +
47B ILE* 3.7 33.4 - - + -
67B LEU* 5.6 0.7 - - + -
69B LEU* 3.8 14.6 - - + -
268B THR* 3.1 19.4 + - + +
269B ASN* 3.6 4.5 - - - +
271B VAL* 1.3 79.2 - - + +
273B LYS* 1.3 65.1 + - - +
274B LEU 3.2 0.9 + - - -
276B SER* 2.8 39.5 + - - +
277B GLU 4.9 0.2 + - - -
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Residues in contact with LYS 273 (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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159B GLU* 3.1 31.9 + - - +
269B ASN 2.7 23.2 + - - +
270B LEU* 3.8 9.4 - - - +
272B VAL* 1.3 74.3 - - - +
274B LEU* 1.3 76.7 + - + +
277B GLU* 4.2 9.4 - - - +
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Residues in contact with LEU 274 (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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159B GLU* 4.4 6.1 - - - +
162B LEU* 3.9 19.7 - - + -
163B ASP* 3.1 52.7 - - + +
166B ALA* 3.6 15.8 - - + +
170B LEU* 4.8 1.2 - - - +
270B LEU* 3.5 26.7 - - + +
271B VAL 2.8 11.2 + - - +
273B LYS* 1.3 96.5 - - + +
275B PHE* 1.3 68.7 + - + +
277B GLU* 3.0 28.5 - - - +
278B VAL* 5.0 1.2 - - - +
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Residues in contact with PHE 275 (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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69B LEU* 4.0 15.9 - - + -
71B ASN* 2.9 20.3 + - - -
73B ILE* 4.0 8.9 - - + +
90B LEU* 4.1 24.0 - - + -
162B LEU* 3.7 42.0 - - + -
165B PHE* 4.2 7.6 - + - -
166B ALA* 3.7 25.1 - - + -
169B PHE* 4.7 2.2 - + - -
256B VAL* 4.3 24.5 - - + -
271B VAL* 2.7 41.2 + - + +
272B VAL 3.6 0.2 + - - -
274B LEU* 1.3 85.0 - - + +
276B SER* 1.3 61.9 + - - +
277B GLU 3.1 2.5 - - - -
278B VAL* 3.2 25.4 + - + +
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Residues in contact with SER 276 (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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46B ALA* 4.1 19.8 + - - +
69B LEU* 4.1 8.5 - - - +
70B ALA* 6.2 2.2 - - - -
71B ASN* 3.3 18.7 + - - +
272B VAL* 2.8 42.4 + - - +
275B PHE* 1.3 75.9 - - - +
277B GLU* 1.3 58.0 + - - +
278B VAL 3.2 6.6 + - - +
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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