Contacts of the helix formed by residues 297 - 311 (chain E) in PDB entry 1HVU
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 GLU 297 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296E THR* 1.3 71.7 - - - +
298E GLU* 1.3 68.2 + - - +
300E GLU* 3.6 12.8 - - + -
301E LEU* 2.8 26.0 + - - +
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Residues in contact with GLU 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278E GLN* 3.4 34.6 - - + +
281E LYS* 6.0 1.8 - - + -
296E THR* 3.1 10.8 - - - +
297E GLU* 1.3 80.4 - - - +
299E ALA* 1.3 59.8 + - - +
301E LEU* 3.5 5.0 - - - +
302E GLU* 3.4 12.1 + - - +
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Residues in contact with ALA 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278E GLN* 4.2 17.0 - - - +
279E LEU* 4.7 12.3 - - + +
282E LEU* 5.9 4.7 - - + -
295E LEU* 5.1 8.5 - - + -
296E THR 3.0 12.6 + - - +
298E GLU* 1.3 77.4 - - - +
300E GLU* 1.3 66.5 + - - +
301E LEU 2.9 2.5 - - - -
302E GLU* 2.8 5.8 + - - +
303E LEU* 2.7 29.1 + - + +
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Residues in contact with GLU 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E LEU* 5.1 7.7 - - + +
296E THR 2.8 22.7 + - - +
297E GLU* 3.6 12.1 - - - -
299E ALA* 1.3 72.6 - - - +
301E LEU* 1.3 62.4 + - - +
303E LEU* 4.5 4.1 - - - +
304E ALA* 3.5 22.2 + - - +
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Residues in contact with LEU 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E GLU 2.8 18.7 + - - +
298E GLU 3.5 5.6 - - - +
300E GLU* 1.3 79.1 - - - +
302E GLU* 1.3 57.4 + - - +
304E ALA* 4.0 1.7 - - - +
305E GLU* 2.9 33.4 + - - +
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Residues in contact with GLU 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E LYS 4.5 16.3 - - - +
276E VAL* 6.1 0.2 - - - -
277E ARG 6.1 0.2 - - - +
278E GLN* 4.6 11.0 - - + +
279E LEU* 5.6 4.5 - - + +
298E GLU 3.4 10.6 + - - +
299E ALA* 2.8 15.3 + - - +
301E LEU* 1.3 73.2 - - - +
303E LEU* 1.3 58.5 + - - +
305E GLU* 3.8 4.4 - - - +
306E ASN* 2.8 33.5 + - - +
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Residues in contact with LEU 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E ALA* 2.7 21.2 + - + +
300E GLU* 4.5 3.6 - - - +
302E GLU* 1.3 70.0 - - - +
304E ALA* 1.3 54.7 + - - +
306E ASN* 2.9 7.4 + - - +
307E ARG* 2.7 35.8 + - - +
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Residues in contact with ALA 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E GLU 3.5 17.6 + - - +
301E LEU* 4.0 1.3 - - - +
302E GLU 3.4 0.2 - - - -
303E LEU* 1.3 79.3 - - - +
305E GLU* 1.3 63.9 + - - +
307E ARG* 3.3 9.6 + - - +
308E GLU* 3.3 16.8 + - - +
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Residues in contact with GLU 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301E LEU 2.9 21.7 + - - +
302E GLU* 3.8 5.4 - - - +
304E ALA* 1.3 75.6 - - - +
306E ASN* 1.3 62.6 + - - +
308E GLU* 3.1 22.7 + - - +
309E ILE* 3.5 4.5 + - - +
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Residues in contact with ASN 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E LEU* 6.1 4.9 - - + -
274E ILE* 4.8 20.4 - - + +
275E LYS 5.5 4.7 - - - +
302E GLU 2.8 22.7 + - - +
303E LEU* 3.5 4.7 - - - +
305E GLU* 1.3 69.8 - - - +
307E ARG* 1.3 67.0 + - - +
308E GLU 2.9 1.2 + - - -
309E ILE* 2.9 17.6 + - - +
310E LEU* 3.1 13.2 + - - +
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Residues in contact with ARG 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E ILE 5.1 0.9 - - - +
245E VAL* 6.4 2.0 - - - +
246E LEU* 5.9 11.7 - - + +
303E LEU 2.7 16.9 + - - +
304E ALA* 3.5 14.1 - - - +
305E GLU 3.3 0.2 - - - -
306E ASN* 1.3 73.1 - - - +
308E GLU* 1.3 65.5 + - - +
310E LEU* 3.5 15.7 + - - +
311E LYS* 3.9 6.4 + - - +
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Residues in contact with GLU 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304E ALA 3.3 7.1 + - - +
305E GLU* 3.1 14.9 + - - +
306E ASN 2.9 1.4 + - - -
307E ARG* 1.3 79.4 - - - +
309E ILE* 1.3 58.5 + - - +
311E LYS* 2.8 28.5 + - - +
312E GLU* 3.5 6.0 + - - +
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Residues in contact with ILE 309 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271E TYR* 4.7 18.5 - - + +
273E GLY* 5.8 3.4 - - - -
274E ILE* 5.5 10.8 - - + +
305E GLU 3.5 4.4 + - - +
306E ASN* 2.9 10.2 + - - +
308E GLU* 1.3 79.0 - - - +
310E LEU* 1.3 58.6 + - - +
311E LYS 3.0 2.2 + - - -
312E GLU* 3.1 29.8 + - + +
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Residues in contact with LEU 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E PRO* 4.5 2.6 - - - +
244E ILE* 3.2 47.8 + - + +
245E VAL* 5.3 0.9 - - - -
306E ASN 3.1 11.1 + - - +
307E ARG* 3.9 12.1 - - - +
308E GLU 3.0 1.0 + - - -
309E ILE* 1.3 75.2 - - - +
311E LYS* 1.3 57.4 + - - +
312E GLU 3.6 0.7 - - - -
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Residues in contact with LYS 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E PRO* 5.1 14.4 - - + -
244E ILE 5.6 1.1 - - - +
307E ARG 3.9 5.4 + - - +
308E GLU 2.8 10.7 + - - +
310E LEU* 1.3 81.4 - - - +
312E GLU* 1.3 58.7 + - - +
313E PRO 3.9 1.9 - - - -
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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