Contacts of the helix formed by residues 290 - 304 (chain A) in PDB entry 4P4P
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 SER 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A ARG* 3.7 24.1 - - - +
288A THR 3.6 0.8 + - - -
289A GLY* 1.3 78.1 + - - -
291A LYS* 1.3 59.4 + - - +
292A ASN* 3.4 7.1 + - - +
293A PHE* 3.1 18.5 + - - +
294A ASN* 2.9 25.3 + - - -
374A ARG 3.0 24.3 + - - -
375A ASP* 4.0 5.7 - - - -
376A PRO* 3.6 7.4 + - - +
7C T 4.2 1.3 - - - -
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Residues in contact with LYS 291 (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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32A LYS* 6.0 3.3 - - - +
290A SER* 1.3 74.5 - - - +
292A ASN* 1.3 83.2 + - - +
294A ASN* 3.2 5.1 + - - +
295A VAL* 3.0 37.0 + - - +
5B A 3.8 18.7 + - - +
7C T 3.7 59.4 - - + +
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Residues in contact with ASN 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A SER* 3.3 7.6 + - - +
291A LYS* 1.3 96.3 + - - +
293A PHE* 1.3 67.3 + - - +
295A VAL* 3.2 7.0 + - - +
296A ILE* 3.0 31.1 + - + +
376A PRO* 4.1 26.4 + - + +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 4.1 11.4 - - + -
289A GLY 3.5 13.2 - - - -
290A SER* 3.1 26.6 + - - +
292A ASN* 1.3 77.3 - - - +
294A ASN* 1.3 72.1 + - - +
296A ILE* 3.3 7.9 + - + +
297A MET* 3.0 61.7 + - + +
361A PHE* 3.5 19.5 - + - -
366A MET* 5.1 6.7 - - + -
369A ALA* 4.6 6.5 - - + -
373A ASN 5.4 0.4 - - - -
374A ARG* 3.6 39.0 - - + +
376A PRO* 3.7 14.0 - - + +
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Residues in contact with ASN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 3.4 18.2 - - - +
286A THR* 2.8 35.3 + - - +
289A GLY* 3.6 3.5 - - - -
290A SER 2.9 13.7 + - - +
291A LYS 3.2 6.9 + - - +
293A PHE* 1.3 83.2 - - - +
295A VAL* 1.3 57.6 + - - +
297A MET* 3.3 4.5 + - - +
298A ARG* 2.8 49.7 + - - +
5B A 4.7 3.4 - - + -
7C T 3.0 33.3 + - - +
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Residues in contact with VAL 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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291A LYS* 3.0 31.8 + - - +
292A ASN* 3.7 9.2 - - - +
293A PHE 3.2 0.2 - - - -
294A ASN* 1.3 76.1 - - - +
296A ILE* 1.3 55.1 + - + +
298A ARG* 3.2 3.0 + - - +
299A GLN* 2.8 57.8 + - + +
5B A 3.8 56.1 - - + +
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Residues in contact with ILE 296 (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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292A ASN* 3.0 23.6 + - + +
293A PHE* 3.6 6.7 - - + +
295A VAL* 1.3 77.5 - - + +
297A MET* 1.3 58.5 + - - +
299A GLN* 3.4 18.1 + - - +
300A ALA* 3.0 26.9 + - + +
366A MET* 4.7 13.7 - - + -
376A PRO* 4.1 26.7 - - + -
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Residues in contact with MET 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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285A LEU* 4.2 12.1 - - - -
293A PHE* 3.0 55.2 + - + +
294A ASN* 3.9 6.1 - - - +
296A ILE* 1.3 77.9 - - - +
298A ARG* 1.3 58.3 + - - +
300A ALA* 3.3 7.1 + - - +
301A ALA* 2.9 26.2 + - - +
308A LEU* 3.5 24.2 - - + -
360A VAL* 4.1 14.1 - - - -
361A PHE* 3.2 33.7 - - + -
364A LEU* 3.9 10.7 - - + +
366A MET* 3.8 18.4 - - + -
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Residues in contact with ARG 298 (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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286A THR* 3.0 41.6 + - - +
294A ASN* 2.8 29.0 + - - +
295A VAL 3.7 0.2 - - - +
297A MET* 1.3 75.1 - - - +
299A GLN* 1.3 59.6 + - - +
301A ALA* 3.3 7.6 + - - +
302A ILE* 2.9 31.9 + - - +
308A LEU* 3.5 35.8 + - + +
309A ASN* 3.8 12.8 - - - +
310A GLU* 3.8 6.1 + - - -
5B A 2.9 66.1 + - - +
6B G 2.9 31.9 + - - +
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Residues in contact with GLN 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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295A VAL* 2.8 38.1 + - - +
296A ILE* 3.6 18.9 - - - +
298A ARG* 1.3 74.9 - - - +
300A ALA* 1.3 63.9 + - - +
302A ILE* 3.3 11.0 + - - +
303A SER* 2.9 24.8 + - - -
4B C 4.6 1.4 + - - -
5B A 3.1 34.7 + - - -
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Residues in contact with ALA 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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296A ILE* 3.0 15.1 + - + +
297A MET 3.6 8.1 - - - +
299A GLN* 1.3 74.8 - - - +
301A ALA* 1.3 64.1 + - - +
303A SER* 2.8 24.1 + - - -
304A LYS* 3.2 14.0 + - + +
364A LEU* 4.7 8.7 - - + +
366A MET* 3.7 28.3 - - + -
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Residues in contact with ALA 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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297A MET 2.9 13.8 + - - +
298A ARG 3.4 9.0 - - - +
299A GLN 3.2 0.2 - - - -
300A ALA* 1.3 76.5 - - - +
302A ILE* 1.3 60.6 + - - +
304A LYS* 3.0 9.4 + - - -
306A TYR* 2.8 41.6 + - + +
308A LEU* 3.8 26.5 - - + +
364A LEU* 3.7 20.7 - - + +
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Residues in contact with ILE 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 ARG 2.9 16.6 + - - +
299A GLN* 3.3 9.8 + - + +
301A ALA* 1.3 75.4 - - - +
303A SER* 1.3 64.8 + - - +
305A GLY* 3.0 14.0 + - - -
306A TYR 3.5 10.1 + - - +
4B C 5.2 10.3 - - - -
5B A 3.3 40.2 - - - +
6B G 3.6 18.6 - - - +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLN 2.9 14.1 + - - -
300A ALA* 2.8 20.9 + - - -
302A ILE* 1.3 79.1 - - - +
304A LYS* 1.3 65.6 + - - +
305A GLY 3.7 0.5 + - - -
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Residues in contact with LYS 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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300A ALA* 3.2 12.3 + - - +
301A ALA 3.0 7.8 + - - +
303A SER* 1.3 84.2 + - - +
305A GLY* 1.3 61.0 + - - +
306A TYR* 3.4 24.0 - - + -
315A LYS* 5.4 4.3 + - - +
363A VAL 4.5 4.9 - - - +
364A LEU* 3.0 44.0 - - + +
365A GLY* 4.4 4.8 - - - +
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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