Contacts of the helix formed by residues 288 - 302 (chain A) in PDB entry 3V4K
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 CYS 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ZN 2.3 38.0 - - - -
257A HIS* 3.5 12.6 - - + -
259A GLU* 4.6 0.2 + - - -
286A SER 3.7 1.6 + - - -
287A PRO* 1.3 75.2 - - - +
289A PHE* 1.3 67.0 + - - +
290A SER* 3.3 24.7 - - - -
291A CYS 3.3 4.0 + - - -
292A ALA* 2.9 20.5 + - - +
315A TYR* 4.1 26.7 - - + -
317A ASP* 6.1 0.2 - - - +
321A CYS* 4.4 2.7 - - - -
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A CYS* 1.3 74.4 - - - +
290A SER* 1.3 70.2 + - - +
292A ALA* 3.2 5.0 + - - +
293A GLN* 2.9 59.5 + - + +
317A ASP* 5.7 2.4 + - - +
320A ARG* 3.2 83.5 - - + +
321A CYS* 4.4 7.7 - - - +
323A GLU* 3.5 24.2 - - + -
324A GLY* 3.6 14.6 - - - -
327A THR* 5.3 5.6 - - + -
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Residues in contact with SER 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A HIS* 5.3 1.4 + - - -
260A LEU* 5.3 1.1 - - - +
288A CYS* 3.3 13.9 - - - -
289A PHE* 1.3 88.6 - - - +
291A CYS* 1.3 63.7 + - - +
293A GLN* 3.5 11.5 + - - +
294A GLU* 3.1 22.7 + - - +
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Residues in contact with CYS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ZN 2.3 35.2 - - - -
257A HIS* 3.5 19.7 - - - -
259A GLU* 3.8 26.2 - - + -
260A LEU* 3.9 17.4 - - - +
287A PRO* 4.1 7.0 - - + -
288A CYS* 3.3 6.0 + - - +
289A PHE 3.2 0.2 - - - -
290A SER* 1.3 80.3 + - - +
292A ALA* 1.3 64.6 + - - +
294A GLU* 3.2 7.4 + - - +
295A MET* 2.9 29.9 + - - +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PRO* 4.0 14.0 - - + +
288A CYS 2.9 18.2 + - - +
289A PHE 3.6 3.8 - - - +
291A CYS* 1.3 75.4 - - - +
293A GLN* 1.3 58.5 + - - +
295A MET* 3.4 2.6 + - - +
296A ALA* 2.9 29.6 + - - +
324A GLY* 3.5 35.0 - - - +
325A LEU* 4.5 0.7 - - - +
327A THR* 5.8 0.2 - - - -
328A LEU* 3.9 20.8 - - + +
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Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 2.9 51.1 + - + +
290A SER* 3.6 10.8 + - - +
291A CYS 3.2 0.2 - - - -
292A ALA* 1.3 77.4 - - - +
294A GLU* 1.3 58.0 + - - +
296A ALA* 3.4 7.7 + - - +
297A LYS* 3.0 28.3 + - + +
320A ARG* 5.1 1.0 + - - -
324A GLY* 5.4 0.6 - - - -
327A THR* 5.2 8.1 - - + -
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Residues in contact with GLU 294 (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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260A LEU* 3.9 22.0 - - + -
263A LEU* 3.8 16.7 - - + +
290A SER 3.1 16.8 + - - +
291A CYS 3.2 3.8 + - - +
293A GLN* 1.3 77.6 - - - +
295A MET* 1.3 57.0 + - - +
297A LYS* 3.3 12.5 + - - +
298A PHE* 2.9 28.6 + - - +
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Residues in contact with MET 295 (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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220A LEU* 5.7 1.8 - - + -
259A GLU* 3.9 32.1 - - + -
262A PHE* 4.5 20.2 - - + -
263A LEU* 4.0 22.9 - - + -
281A CYS* 5.4 2.7 - - + -
287A PRO* 4.1 18.6 - - + -
291A CYS 2.9 20.0 + - - +
292A ALA 3.7 0.7 - - - +
294A GLU* 1.3 74.3 - - - +
296A ALA* 1.3 64.1 + - - +
298A PHE* 3.3 3.8 + - - +
299A ILE* 3.0 28.2 + - - +
307A LEU* 4.1 15.0 - - + -
309A ILE* 3.8 25.1 - - + -
328A LEU* 3.7 18.4 - - + -
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA 2.9 18.8 + - - +
293A GLN 3.6 4.9 - - - +
295A MET* 1.3 71.0 - - - +
297A LYS* 1.3 66.2 + - - +
299A ILE* 3.4 7.4 + - - +
300A SER* 2.7 30.6 + - - +
327A THR* 4.1 25.1 - - + +
328A LEU* 3.6 10.2 - - - +
331A ALA* 3.9 16.8 - - + +
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Residues in contact with LYS 297 (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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293A GLN* 3.0 14.3 + - + +
294A GLU* 3.3 18.4 + - - +
296A ALA* 1.3 76.2 - - - +
298A PHE* 1.3 63.6 + - - +
300A SER* 3.3 7.8 + - - -
301A LYS* 3.1 23.2 + - - +
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Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 3.8 42.8 - - + -
266A ILE* 3.6 41.1 - - + -
267A PRO* 4.8 9.9 - - + -
294A GLU* 2.9 16.5 + - - +
295A MET 3.3 4.9 + - - +
297A LYS* 1.3 76.5 - - - +
299A ILE* 1.3 74.4 + - + +
301A LYS* 3.1 2.9 + - - -
302A ASN* 2.9 63.8 + - + +
304A HIS* 6.0 0.4 - + - -
305A VAL* 4.6 13.2 - - + -
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Residues in contact with ILE 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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263A LEU* 6.2 0.4 - - + -
295A MET* 3.0 16.1 + - - +
296A ALA* 3.6 6.3 - - - +
298A PHE* 1.3 88.7 - - + +
300A SER* 1.3 64.2 + - - +
301A LYS 3.4 0.3 + - - -
302A ASN 3.4 20.2 + - - +
303A LYS* 4.0 11.3 + - - -
305A VAL* 4.7 17.7 - - + +
307A LEU* 4.0 29.8 - - + +
328A LEU* 4.1 10.5 - - + -
331A ALA* 3.7 26.8 - - + +
332A GLY 4.3 1.1 - - - -
333A ALA* 3.6 39.5 - - + +
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Residues in contact with SER 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ALA 2.7 23.5 + - - -
297A LYS* 3.6 8.0 - - - -
299A ILE* 1.3 79.1 - - - +
301A LYS* 1.3 57.6 + - - +
303A LYS* 4.2 19.0 - - - +
331A ALA* 3.9 16.1 + - - +
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Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LYS 3.1 15.4 + - - +
298A PHE* 3.1 4.7 + - - +
300A SER* 1.3 75.9 - - - +
302A ASN* 1.3 69.3 + - - +
303A LYS* 3.8 3.7 + - - -
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Residues in contact with ASN 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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273A LEU* 5.5 0.7 - - - +
298A PHE* 2.9 67.3 + - + +
299A ILE* 3.4 9.8 + - - +
301A LYS* 1.3 89.6 - - - +
303A LYS* 1.3 55.9 + - - +
304A HIS* 3.2 33.2 - - + -
305A VAL* 3.0 25.1 + - + +
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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