Contacts of the helix formed by residues 319 - 328 (chain B) in PDB entry 5HMS
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 TYR 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B HIS* 3.9 21.1 - + - -
282B PHE* 2.5 65.1 + + - -
285B LEU* 3.7 5.9 - - + +
286B TRP* 3.3 32.7 + + - +
296B LEU* 3.7 9.9 - - + +
300B VAL* 3.7 44.4 - - + -
317B THR* 3.0 11.9 + - - +
318B TYR* 1.3 75.8 - - - +
320B THR* 1.3 64.8 + - - +
321B PRO* 3.1 3.7 - - - -
322B GLN* 3.3 24.8 + - + +
323B LEU* 2.9 25.8 + - + +
326B TRP* 5.0 0.2 - + - -
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Residues in contact with THR 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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31B LEU* 3.8 26.0 - - + +
32B ILE 3.3 14.0 + - - -
33B TYR* 3.8 9.6 - - + +
73B LEU* 3.9 28.0 - - + -
317B THR* 2.6 30.6 + - - +
318B TYR 3.2 0.4 - - - -
319B TYR* 1.3 74.4 - - - +
321B PRO* 1.3 72.7 - - + +
323B LEU* 3.2 9.9 + - - +
324B LEU* 3.0 30.4 + - + +
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Residues in contact with PRO 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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33B TYR* 3.6 27.6 - - + +
68B LEU* 3.8 34.8 - - + +
71B GLU* 5.1 0.3 - - - +
318B TYR 3.7 5.2 - - - +
319B TYR 3.5 3.1 - - - -
320B THR* 1.3 95.9 - - + +
322B GLN* 1.3 71.9 + - - +
324B LEU* 3.1 21.4 + - + +
325B GLN* 3.6 12.3 + - - +
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Residues in contact with GLN 322 (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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282B PHE* 5.1 2.4 - - - -
286B TRP* 4.0 25.2 - - - -
296B LEU* 5.0 2.6 - - - +
318B TYR 4.0 4.7 - - - +
319B TYR* 3.5 35.7 - - + +
321B PRO* 1.3 88.5 - - - +
323B LEU* 1.3 55.8 + - - +
325B GLN* 3.3 17.7 + - - +
326B TRP* 3.0 68.9 + - + +
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Residues in contact with LEU 323 (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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26B LEU* 4.3 6.3 - - + -
31B LEU* 3.7 37.2 - - + -
300B VAL* 3.7 23.8 - - + -
301B LEU* 4.0 25.1 - - + -
304B MET* 4.0 18.4 - - + -
317B THR* 3.8 17.9 - - + -
319B TYR* 2.9 25.3 + - + +
320B THR 3.4 5.2 - - - +
322B GLN* 1.3 74.5 - - - +
324B LEU* 1.3 64.7 + - - +
326B TRP* 3.9 6.9 - - + +
327B LEU* 3.1 32.1 + - + +
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Residues in contact with LEU 324 (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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28B ALA* 3.8 27.8 - - + +
31B LEU* 4.7 7.6 - - + -
68B LEU* 4.1 19.5 - - + +
71B GLU* 3.8 23.6 - - + +
72B GLY 3.8 2.2 - - - -
73B LEU* 3.8 36.6 - - + +
320B THR* 3.0 36.6 + - + +
321B PRO* 3.1 11.1 + - + +
323B LEU* 1.3 75.9 - - - +
325B GLN* 1.3 62.1 + - - +
327B LEU* 3.9 6.0 + - + +
328B LYS* 3.3 28.9 + - + +
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Residues in contact with GLN 325 (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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71B GLU* 3.0 24.1 + - - +
321B PRO 3.6 9.8 + - - +
322B GLN* 3.3 18.9 + - - +
323B LEU 3.3 0.4 - - - -
324B LEU* 1.3 77.2 - - - +
326B TRP* 1.3 70.2 + - + +
328B LYS* 2.8 34.0 + - - +
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Residues in contact with TRP 326 (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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296B LEU* 4.3 17.9 - - + -
297B LYS* 3.6 76.5 + - + +
300B VAL* 3.9 27.6 - - + -
301B LEU* 4.8 14.6 - - + +
319B TYR* 5.1 0.2 - + - -
322B GLN* 3.0 53.4 + - + +
323B LEU* 3.4 16.4 + - + +
325B GLN* 1.3 91.1 + - + +
327B LEU* 1.3 63.3 + - - +
328B LYS 4.3 2.9 - - - +
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Residues in contact with LEU 327 (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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26B LEU* 3.2 49.8 - - + +
27B ASN* 3.9 25.6 - - + +
28B ALA* 4.0 5.8 - - + +
31B LEU* 4.5 11.9 - - + -
301B LEU* 5.5 6.3 - - + -
323B LEU* 3.1 27.1 + - + +
324B LEU* 4.0 10.1 - - + +
326B TRP* 1.3 78.6 - - - +
328B LYS* 1.3 66.9 + - + +
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Residues in contact with LYS 328 (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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70B GLU 5.4 1.3 - - - -
71B GLU* 3.4 47.5 + - + +
324B LEU* 3.3 16.3 + - + +
325B GLN* 2.8 23.5 + - - +
326B TRP 4.3 2.6 - - - +
327B LEU* 1.3 81.3 - - + +
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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