Contacts of the helix formed by residues 302 - 316 (chain B) in PDB entry 3H2U
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 302 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B CYS* 4.1 2.9 - - - -
268B GLU* 3.4 20.6 - - - +
300B GLY 4.1 4.5 - - - +
301B PRO* 1.3 86.1 - - + +
303B GLY* 1.3 67.6 - - - +
304B ARG* 3.2 6.3 - - + +
305B SER* 2.9 32.2 + - - +
306B MET* 3.1 9.9 + - - +
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Residues in contact with GLY 303 (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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222B CYS* 3.6 14.3 - - - -
250B PHE* 3.7 29.4 - - - -
266B VAL* 4.0 6.7 - - - +
268B GLU* 2.8 16.8 + - - -
302B PRO* 1.3 69.3 - - - +
304B ARG* 1.3 62.1 + - - +
306B MET* 3.9 0.7 - - - +
307B LEU* 3.0 28.1 + - - +
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Residues in contact with ARG 304 (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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250B PHE* 3.5 27.3 - - + -
252B GLN* 6.2 1.6 - - - +
302B PRO* 4.6 4.7 - - + +
303B GLY* 1.3 76.6 - - - +
305B SER* 1.3 64.2 + - - +
307B LEU* 3.7 3.9 - - - +
308B ALA* 3.4 18.0 + - - +
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Residues in contact with SER 305 (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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301B PRO* 4.0 11.2 - - - -
302B PRO* 2.9 31.8 + - - +
304B ARG* 1.3 75.8 - - - +
306B MET* 1.3 56.7 + - - +
307B LEU 3.2 0.2 - - - -
308B ALA* 3.0 7.5 + - - +
309B ALA* 2.7 37.1 + - - +
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Residues in contact with MET 306 (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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204B TYR* 3.4 32.1 - - + +
206B HIS* 5.9 0.7 - - - -
222B CYS* 5.0 3.8 - - + -
266B VAL* 4.1 7.9 - - + -
297B CYS* 3.7 39.3 - - + -
298B ALA* 4.4 14.6 - - - +
301B PRO* 4.1 18.4 - - + +
302B PRO 3.1 16.6 + - - +
303B GLY* 3.9 3.4 - - - +
305B SER* 1.3 74.4 - - - +
307B LEU* 1.3 54.9 + - - +
309B ALA* 3.3 4.4 - - + +
310B LEU* 2.6 80.1 + - + +
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Residues in contact with LEU 307 (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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250B PHE* 4.1 4.9 - - + -
252B GLN* 3.6 34.1 - - + +
253B LEU 3.5 20.9 - - - +
254B ALA* 4.0 13.7 - - - +
264B PHE* 4.1 6.7 - - + -
266B VAL* 3.9 28.2 - - + +
303B GLY 3.0 17.7 + - - +
304B ARG* 3.7 5.4 - - - +
306B MET* 1.3 78.0 - - - +
308B ALA* 1.3 57.1 + - - +
310B LEU* 3.8 1.2 - - - -
311B ILE* 2.8 65.9 + - + +
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Residues in contact with ALA 308 (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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304B ARG 3.4 9.4 + - - +
305B SER* 3.0 10.1 + - - +
307B LEU* 1.3 76.4 - - - +
309B ALA* 1.3 56.7 + - - +
311B ILE* 2.8 12.9 + - - +
312B ALA* 2.7 38.4 + - - +
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Residues in contact with ALA 309 (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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204B TYR* 3.5 25.0 - - - +
301B PRO* 6.3 1.3 - - + -
305B SER 2.7 22.6 + - - +
306B MET* 3.3 11.7 - - + +
308B ALA* 1.3 72.0 - - - +
310B LEU* 1.3 58.1 + - - +
312B ALA* 3.3 5.4 + - - +
313B ALA* 2.9 31.4 + - - +
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Residues in contact with LEU 310 (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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204B TYR* 3.6 28.5 - - + -
224B CYS* 4.4 9.4 - - + -
264B PHE* 3.8 22.0 - - + -
266B VAL* 3.9 19.5 - - + -
297B CYS* 4.3 9.9 - - - -
306B MET* 2.6 57.1 + - + +
307B LEU 3.9 0.4 - - - +
309B ALA* 1.3 70.1 - - - +
311B ILE* 1.3 67.0 + - - +
313B ALA* 4.3 2.9 - - + -
314B GLN* 3.0 28.8 + - - +
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Residues in contact with ILE 311 (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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254B ALA* 4.2 11.4 - - + -
255B CYS 4.1 23.1 - - - +
256B GLY* 5.0 8.1 - - - -
257B GLN* 5.7 2.0 - - + +
262B LYS* 4.6 8.7 - - + -
264B PHE* 4.0 8.9 - - + -
307B LEU* 2.8 55.5 + - + +
308B ALA* 2.8 12.7 + - - +
310B LEU* 1.3 72.1 - - - +
312B ALA* 1.3 58.4 + - - +
314B GLN* 3.8 11.9 + - - +
315B ALA* 3.0 29.2 + - + +
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Residues in contact with ALA 312 (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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308B ALA 2.7 18.2 + - - +
309B ALA* 3.7 6.1 - - - +
311B ILE* 1.3 74.1 - - + +
313B ALA* 1.3 62.1 + - - +
315B ALA* 2.8 22.3 - - - +
316B THR* 3.2 17.3 + - + +
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Residues in contact with ALA 313 (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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194B LEU* 4.4 19.5 - - + +
204B TYR* 4.0 26.9 - - + -
309B ALA 2.9 17.8 + - - +
310B LEU* 3.3 4.9 + - + +
312B ALA* 1.3 72.6 - - - +
314B GLN* 1.3 63.3 + - - +
315B ALA 2.9 4.2 + - - -
316B THR* 2.8 28.5 + - - -
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Residues in contact with GLN 314 (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 LYS* 3.5 44.0 - - - +
263B GLY 5.1 1.0 + - - -
264B PHE* 3.7 19.9 - - + -
310B LEU 3.0 9.9 + - - +
311B ILE* 3.8 14.3 + - - +
313B ALA* 1.3 78.7 - - - +
315B ALA* 1.3 62.3 + - - +
317B ALA* 3.4 19.4 - - - +
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Residues in contact with ALA 315 (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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311B ILE* 3.0 20.1 + - + +
312B ALA* 2.8 22.4 - - - +
314B GLN* 1.3 75.5 - - - +
316B THR* 1.3 51.2 + - + +
317B ALA* 2.3 25.1 + - - +
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Residues in contact with THR 316 (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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194B LEU* 5.3 6.6 - - - +
312B ALA 3.2 15.0 - - - +
313B ALA* 2.8 20.6 + - - -
315B ALA* 1.3 70.6 - - + +
317B ALA* 1.3 61.7 + - - +
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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