Contacts of the helix formed by residues 261 - 270 (chain B) in PDB entry 1H3F
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B VAL* 3.8 40.8 - - + +
226B GLY 3.4 25.4 - - - +
229B GLY* 4.0 11.7 - - - +
257B VAL* 3.9 7.9 - - + -
258B PRO* 2.8 33.0 + - + +
260B PRO* 1.3 84.4 - - + +
262B LEU* 1.3 63.5 + - - -
263B PRO* 3.3 3.1 - - - -
264B SER* 2.8 29.3 + - - +
265B TYR* 3.0 19.7 + - + +
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 4.5 5.3 - - + +
258B PRO 3.6 2.5 + - - +
259B ASP* 3.2 20.0 + - - +
261B LEU* 1.3 75.4 - - - +
263B PRO* 1.3 72.1 - - + +
265B TYR* 3.1 6.0 + - - +
266B PHE* 3.0 38.9 + - + -
281B LEU* 4.0 15.7 - - + -
285B PRO* 4.3 9.4 - - + +
288B ALA* 4.0 17.5 - - + -
289B HIS* 3.7 47.3 - - + +
292B LEU* 4.1 23.3 - - + -
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Residues in contact with PRO 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A SO4 3.7 21.1 - - - +
259B ASP 4.0 3.8 - - - +
260B PRO 3.6 11.9 - - - +
261B LEU 3.4 3.6 - - - -
262B LEU* 1.3 95.8 - - + +
264B SER* 1.3 56.5 + - - +
266B PHE* 3.3 8.6 + - + +
267B ARG* 3.0 54.3 + - + +
277B ILE* 4.8 5.5 - - + +
281B LEU* 3.8 26.2 - - + -
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Residues in contact with SER 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A SO4 4.5 4.2 + - - -
224B LEU* 5.0 1.6 - - - +
225B VAL* 5.7 2.8 + - - +
260B PRO 5.8 0.2 - - - -
261B LEU* 2.8 32.4 + - - +
263B PRO* 1.3 79.4 - - - +
265B TYR* 1.3 65.4 + - - +
267B ARG* 3.8 21.7 - - - +
268B LEU* 2.9 49.1 + - - +
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Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.7 4.3 - - + -
224B LEU* 3.6 24.9 - - + -
225B VAL 2.7 27.0 + - - -
226B GLY 4.2 6.1 - - - -
227B LEU* 4.5 2.4 + - - +
233B MET* 3.4 16.9 - - + +
241B ILE* 5.1 0.9 - - + -
254B LEU* 4.6 8.3 - - + -
257B VAL* 3.5 36.3 - - + +
261B LEU* 3.0 34.5 + - + +
262B LEU* 3.5 9.0 - - - +
264B SER* 1.3 78.4 + - - +
266B PHE* 1.3 61.1 + - - +
269B LEU* 2.9 60.6 + - + +
270B THR* 3.9 1.4 + - - +
292B LEU* 4.2 22.4 - - + +
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Residues in contact with PHE 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 LEU* 3.0 43.3 + - + -
263B PRO 3.7 4.0 - - - +
265B TYR* 1.3 76.8 - - - +
267B ARG* 1.3 57.0 + - - +
270B THR* 2.6 41.8 + - + +
272B LEU* 4.0 19.8 + - + +
277B ILE* 3.4 38.3 - - + +
280B LEU* 3.9 24.5 - - + -
281B LEU* 4.4 7.6 - - + -
288B ALA* 3.5 32.8 - - + -
291B VAL 4.9 0.9 - - - -
292B LEU* 3.7 34.1 - - + -
295B LEU* 5.2 0.7 - - + -
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Residues in contact with ARG 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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504A SO4 3.0 41.6 + - - -
17B ARG* 5.6 4.6 - - - +
18B GLY* 4.6 15.3 - - - -
60B ARG* 5.1 1.0 + - - -
263B PRO* 3.0 32.8 + - - +
264B SER* 3.8 19.7 - - - +
266B PHE* 1.3 78.6 - - - +
268B LEU* 1.3 68.9 + - + +
270B THR 3.6 9.6 - - - +
272B LEU 5.9 0.7 - - - -
274B GLU* 4.1 21.5 + - - +
277B ILE* 4.0 17.5 - - + -
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Residues in contact with LEU 268 (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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18B GLY* 3.7 27.1 - - - +
56B ALA 4.9 0.3 - - - +
57B VAL* 4.0 38.0 - - + +
60B ARG* 4.6 8.5 + - - +
221B MET* 4.6 2.5 - - + -
222B PRO* 3.8 36.1 - - + +
223B LEU 5.0 1.1 - - - +
224B LEU* 4.2 24.5 - - + -
264B SER* 2.9 31.6 + - - +
267B ARG* 1.3 85.9 - - + +
269B LEU* 1.3 66.0 + - - +
270B THR 3.8 0.4 - - - -
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.7 39.5 - - + +
56B ALA* 4.3 13.7 - - + -
57B VAL* 4.2 9.2 - - + -
60B ARG* 3.4 19.5 + - - +
224B LEU* 4.1 11.2 - - + -
265B TYR* 2.9 48.7 + - + +
268B LEU* 1.3 86.0 - - - +
270B THR* 1.3 63.9 + - + +
296B LEU* 3.6 40.9 - - + +
300B TYR* 5.4 1.9 + - + +
309B ILE* 3.7 6.4 - - - +
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Residues in contact with THR 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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17B ARG* 5.9 0.2 + - - -
60B ARG* 3.2 15.4 + - - +
265B TYR 4.4 1.8 - - - +
266B PHE* 2.6 43.0 + - + +
267B ARG* 3.6 10.6 - - - +
269B LEU* 1.3 82.9 - - - +
271B ASP* 1.3 60.9 + - - +
272B LEU* 3.4 21.9 + - - +
292B LEU* 4.4 11.0 - - + -
295B LEU* 4.3 17.7 - - + -
296B LEU* 4.3 13.7 - - + -
309B ILE* 3.6 17.3 - - + -
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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