Contacts of the helix formed by residues 310 - 321 (chain B) in PDB entry 1Q5K
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 310 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B VAL* 4.1 38.4 - - + -
159B LYS* 5.7 3.1 - - - +
251B LEU* 5.3 1.6 - - + -
306B ARG* 5.6 0.7 - - - +
308B ARG 3.6 8.1 - - - +
309B THR* 1.3 92.7 - - + +
311B PRO* 1.3 73.2 - - + +
312B GLU* 3.9 12.1 - - - +
313B ALA* 3.0 30.6 + - + +
314B ILE* 3.3 5.2 + - - +
339B PHE* 4.6 6.1 - - + -
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Residues in contact with PRO 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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309B THR 3.3 6.5 - - - +
310B PRO* 1.3 83.5 - - + +
312B GLU* 1.3 73.7 + - - +
314B ILE* 3.1 13.4 + - + +
315B ALA* 2.9 27.5 + - - +
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Residues in contact with GLU 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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310B PRO* 3.9 8.5 - - - +
311B PRO* 1.3 95.1 - - - +
313B ALA* 1.3 56.8 + - - +
315B ALA* 4.1 7.2 - - - -
316B LEU* 2.9 26.2 + - - +
337B HIS* 3.2 10.4 + - - -
338B SER* 3.5 24.9 - - - +
339B PHE* 3.7 27.8 - - + +
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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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247B LEU* 4.3 1.7 - - - +
251B LEU* 3.8 22.9 - - + -
309B THR* 4.3 5.6 - - + -
310B PRO* 3.0 18.8 + - + +
312B GLU* 1.3 78.3 - - - +
314B ILE* 1.3 58.7 + - - +
316B LEU* 3.4 3.4 + - - +
317B CYS* 3.0 33.9 + - - -
339B PHE* 3.5 35.0 - - + -
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Residues in contact with ILE 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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301B TRP* 4.0 40.7 - - + +
302B THR* 4.2 25.1 - - + +
305B PHE* 3.6 27.8 - - + +
309B THR* 3.9 26.5 - - + +
310B PRO 3.9 4.0 - - - +
311B PRO* 3.1 13.6 + - + +
313B ALA* 1.3 74.3 - - - +
315B ALA* 1.3 64.8 + - - +
317B CYS* 3.4 7.2 + - - +
318B SER* 3.1 22.3 + - - -
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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 PRO 2.9 12.8 + - - +
312B GLU* 3.6 11.2 - - - +
313B ALA 3.3 0.2 - - - -
314B ILE* 1.3 75.9 - - - +
316B LEU* 1.3 64.9 + - - +
318B SER* 2.7 24.5 + - - -
319B ARG* 3.2 15.0 + - + +
337B HIS* 4.0 14.6 - - + +
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Residues in contact with LEU 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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166B PHE* 4.5 4.7 - - + -
247B LEU* 3.7 19.5 - - + -
312B GLU 2.9 17.6 + - - +
313B ALA 3.6 5.2 - - - +
314B ILE 3.3 0.2 - - - -
315B ALA* 1.3 76.3 - - - +
317B CYS* 1.3 63.9 + - - +
319B ARG* 3.0 11.2 + - - -
320B LEU* 3.1 31.0 + - + +
329B LEU* 3.6 26.9 - - + -
334B ALA* 4.5 5.4 - - + -
337B HIS* 3.6 22.1 + - + +
339B PHE* 3.7 29.4 - - + -
340B PHE* 3.7 22.0 - - + -
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Residues in contact with CYS 317 (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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244B GLY 4.7 1.8 - - - -
247B LEU* 3.6 28.7 - - - -
248B ALA* 4.0 14.4 - - - -
251B LEU* 4.0 3.8 - - - -
301B TRP* 4.1 20.4 - - + -
305B PHE* 3.8 23.1 - - + -
313B ALA 3.0 17.1 + - - +
314B ILE* 3.6 9.4 - - - +
315B ALA 3.3 0.2 - - - -
316B LEU* 1.3 76.6 - - - +
318B SER* 1.3 57.7 + - - +
320B LEU* 3.1 5.3 + - - +
321B LEU* 2.9 37.9 + - + +
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Residues in contact with SER 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B TRP* 3.5 37.0 + - - +
314B ILE* 3.1 12.2 + - - -
315B ALA* 2.7 24.4 + - - -
317B CYS* 1.3 77.5 - - - +
319B ARG* 1.3 63.1 + - - +
320B LEU 3.4 0.4 + - - -
321B LEU 3.9 5.9 - - - +
322B GLU* 3.2 25.6 - - - +
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Residues in contact with ARG 319 (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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315B ALA* 3.3 17.7 - - + +
316B LEU* 3.0 5.6 + - - +
318B SER* 1.3 81.6 + - - +
320B LEU* 1.3 61.0 + - - +
322B GLU* 3.2 25.1 + - - +
327B ALA* 3.1 27.7 + - - +
328B ARG* 3.5 5.2 - - - -
329B LEU* 3.1 59.8 + - + +
337B HIS* 5.2 5.8 - - + -
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Residues in contact with LEU 320 (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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166B PHE* 3.5 33.9 - - + -
240B VAL* 3.6 27.8 - - + +
241B TRP* 4.2 6.9 - - - -
244B GLY* 3.7 27.1 - - - -
247B LEU* 4.0 11.2 - - + -
316B LEU* 3.1 43.1 + - + +
317B CYS* 3.7 2.9 - - - +
319B ARG* 1.3 80.4 - - - +
321B LEU* 1.3 59.9 + - - +
322B GLU 3.2 6.9 + - - -
328B ARG* 3.2 23.0 + - - +
329B LEU* 4.1 13.9 - - + -
334B ALA* 4.2 4.3 - - + -
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Residues in contact with LEU 321 (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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241B TRP* 3.3 62.1 - - + +
244B GLY* 3.8 21.8 - - - +
245B CYS* 3.8 10.8 - - - +
248B ALA* 4.5 9.6 - - + -
256B ILE* 4.7 0.4 - - + -
257B PHE* 4.0 14.6 - - + -
273B LEU* 3.4 20.4 - - + +
301B TRP* 3.6 32.4 + - + -
317B CYS* 2.9 14.8 + - + +
318B SER 3.9 7.3 - - - +
320B LEU* 1.3 74.1 - - - +
322B GLU* 1.3 60.7 + - - +
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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