Contacts of the helix formed by residues 298 - 308 (chain A) in PDB entry 1VPE
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 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A ASP* 3.4 9.2 - - - +
267A VAL* 4.7 3.1 - - + -
280A VAL* 3.7 29.6 - - + -
297A GLY* 1.4 82.6 - - - +
299A GLU* 1.3 65.1 + - + +
301A ILE* 3.5 14.3 + - + +
302A GLU* 3.3 27.7 + - - +
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A VAL* 3.7 16.3 - - + +
265A ASP* 3.0 25.3 + - - +
280A VAL* 5.5 1.2 - - - +
282A ARG* 2.9 52.4 + - - +
298A PRO* 1.3 78.5 - - + +
300A THR* 1.3 65.7 + - - +
302A GLU* 3.0 9.8 + - - +
303A LEU* 3.0 19.4 + - - +
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LEU 4.9 0.4 - - - +
263A PRO* 3.6 18.3 - - + +
264A VAL* 3.2 15.4 + - - +
265A ASP* 2.7 32.7 + - - -
296A ILE* 4.0 12.6 - - + -
297A GLY 3.2 6.3 + - - -
299A GLU* 1.3 70.8 - - - +
301A ILE* 1.3 58.1 + - - +
303A LEU* 2.9 8.8 + - + +
304A PHE* 2.7 73.9 + - + +
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Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ILE* 3.9 23.6 - - + +
297A GLY 3.0 22.3 + - - +
298A PRO* 3.7 17.3 - - + +
299A GLU 3.2 0.2 - - - -
300A THR* 1.3 74.5 - - - +
302A GLU* 1.3 63.4 + - - +
304A PHE* 4.0 3.3 - - - +
305A LYS* 2.9 48.1 + - + +
330A GLU* 4.2 21.5 - - + +
331A GLY* 4.0 20.6 - - - +
334A GLN* 3.6 28.0 - - + +
335A VAL* 5.4 2.9 - - + +
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A PRO 3.3 13.2 + - - +
299A GLU* 3.0 10.6 + - - +
301A ILE* 1.3 83.6 - - - +
303A LEU* 1.3 59.3 + - - +
305A LYS* 3.5 30.3 + - - +
306A GLN* 3.0 39.9 + - + +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A VAL* 3.8 27.1 - - + -
262A LEU 4.1 12.6 - - - +
264A VAL* 4.3 21.5 - - + -
299A GLU 3.0 12.2 + - - +
300A THR* 2.9 10.7 + - + +
302A GLU* 1.3 73.3 - - - +
304A PHE* 1.3 62.4 + - + +
306A GLN* 3.0 22.5 + - - +
307A LYS* 2.9 48.9 + - + +
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Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A VAL* 5.5 1.1 - - + -
216A LEU* 3.5 31.4 - - + -
217A ILE 3.4 27.6 - - - -
261A VAL* 3.8 33.9 - - + -
262A LEU 4.4 2.5 - - - -
263A PRO* 4.2 3.4 - - + -
296A ILE* 3.9 20.9 - - + -
300A THR* 2.7 41.9 + - + +
301A ILE* 4.0 3.8 - - - +
303A LEU* 1.3 73.4 - - + +
305A LYS* 1.3 57.3 + - + +
307A LYS* 3.3 3.0 + - - +
308A LEU* 2.9 41.8 + - + +
320A MET* 3.8 26.2 - - - -
335A VAL* 4.4 10.1 - - + -
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Residues in contact with LYS 305 (chain A).
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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301A ILE* 2.9 43.2 + - + +
302A GLU* 3.6 28.0 + - - +
303A LEU 3.2 0.2 - - - -
304A PHE* 1.3 74.8 - - - +
306A GLN* 1.3 57.1 + - + +
308A LEU* 3.1 8.6 + - - +
309A SER* 2.8 30.4 + - - -
334A GLN* 4.8 15.6 + - - +
335A VAL* 6.0 1.8 - - + -
338A ALA* 4.1 24.2 - - + +
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Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A GLU* 3.0 33.3 + - + +
303A LEU* 3.0 27.7 + - - +
305A LYS* 1.3 76.7 - - - +
307A LYS* 1.3 67.3 + - + +
308A LEU 3.1 0.5 + - - -
309A SER* 2.7 29.3 + - - -
310A ASP* 4.2 2.6 - - - +
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Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL* 4.0 7.1 - - - +
214A ARG* 2.9 55.6 + - - +
216A LEU* 4.3 15.9 - - + -
259A GLU* 3.2 30.6 + - - -
261A VAL* 3.9 17.9 - - + -
303A LEU* 2.9 41.1 + - + +
304A PHE* 3.3 5.4 + - - +
306A GLN* 1.3 76.1 - - + +
308A LEU* 1.3 57.2 + - - +
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL* 3.9 25.1 - - + -
192A VAL* 4.0 6.7 - - + -
216A LEU* 4.2 10.3 - - + -
304A PHE* 2.9 28.4 + - + +
305A LYS* 3.6 4.3 - - - +
307A LYS* 1.3 76.5 - - - +
309A SER* 1.3 66.4 + - - +
310A ASP 2.9 5.0 + - - -
311A ALA* 3.0 20.2 + - - +
314A VAL* 4.0 30.7 - - + -
335A VAL* 4.5 13.7 - - + -
338A ALA* 4.4 16.6 - - + +
339A ILE* 4.0 21.5 - - + -
342A LEU* 3.4 14.8 - - + +
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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