Contacts of the helix formed by residues 297 - 312 (chain A) in PDB entry 4CSC
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 ALA 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A GLY* 1.3 73.7 - - - -
298A ASP* 1.4 64.7 + - - +
299A ALA* 3.9 7.2 - - + +
300A SER* 3.1 24.2 + - - +
301A LEU* 3.0 22.5 + - - +
352A GLN* 4.2 1.1 - - - -
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Residues in contact with ASP 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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296A GLY 3.9 0.2 + - - -
297A ALA* 1.4 72.2 - - - +
299A ALA* 1.3 57.4 + - - +
301A LEU* 3.3 6.0 - - - +
302A ARG* 2.9 29.0 + - - +
352A GLN* 2.6 33.8 + - - +
355A LYS* 5.9 1.8 - - - +
356A ILE* 3.5 23.6 - - + +
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Residues in contact with ALA 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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297A ALA* 3.1 7.1 - - + +
298A ASP* 1.3 79.3 - - - +
300A SER* 1.3 63.8 + - - +
302A ARG* 3.2 9.7 + - - +
303A ASP* 3.1 26.0 + - - +
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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 GLY* 5.3 2.9 - - - -
297A ALA* 3.1 24.1 + - - +
299A ALA* 1.3 75.5 - - - +
301A LEU* 1.3 66.0 + - - +
303A ASP* 3.1 15.8 + - - +
304A TYR* 3.0 23.8 + - - +
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Residues in contact with LEU 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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288A LEU* 4.4 18.8 - - + +
296A GLY* 4.9 10.3 - - - +
297A ALA 3.0 13.8 + - - +
298A ASP* 3.3 6.1 - - - +
300A SER* 1.3 75.5 - - - +
302A ARG* 1.3 62.4 + - - +
304A TYR* 3.5 7.2 - - - +
305A ILE* 3.0 30.7 + - - +
349A LEU* 4.1 19.1 - - + -
352A GLN* 2.8 45.1 - - + +
353A LEU* 3.9 19.3 - - + -
356A ILE* 3.1 21.8 - - + -
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Residues in contact with ARG 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 ASP 2.9 18.0 + - - +
299A ALA* 3.5 9.4 - - - +
300A SER 3.0 0.6 - - - -
301A LEU* 1.3 77.4 - - - +
303A ASP* 1.3 65.6 + - - +
305A ILE* 3.2 6.2 + - - +
306A TRP* 3.1 32.9 + - + +
356A ILE* 4.3 13.2 - - + -
359A ASN* 5.7 5.3 + - - +
360A VAL* 3.9 22.1 - - + +
363A GLU* 3.2 35.2 + - - -
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Residues in contact with ASP 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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299A ALA 3.1 18.5 + - - +
300A SER* 3.2 16.7 + - - +
302A ARG* 1.3 76.0 - - - +
304A TYR* 1.3 55.9 + - - +
306A TRP* 3.3 9.4 + - - +
307A ASN* 3.0 30.4 + - - +
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Residues in contact with TYR 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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284A TRP* 3.4 42.8 + + - -
287A GLN* 2.9 39.3 - - - +
288A LEU* 3.3 48.0 - - + -
291A ALA* 4.5 15.5 - - + -
300A SER 3.0 8.7 + - - +
301A LEU 3.5 11.4 - - - +
303A ASP* 1.3 78.9 - - - +
305A ILE* 1.3 60.0 + - - +
307A ASN* 3.4 18.7 - - - +
308A THR* 3.3 20.7 + - - -
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Residues in contact with ILE 305 (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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284A TRP* 3.9 17.5 - - + -
288A LEU* 5.9 0.4 - - + -
301A LEU 3.0 16.4 - - - +
302A ARG* 3.2 7.5 + - - +
304A TYR* 1.3 75.7 - - + +
306A TRP* 1.3 62.5 + - - +
307A ASN 3.2 0.2 - - - -
308A THR* 3.2 9.1 + - - -
309A LEU* 3.1 24.5 + - + +
315A VAL* 4.2 20.0 - - + -
353A LEU* 4.2 11.0 - - + -
356A ILE* 3.9 19.5 - - + -
357A VAL* 3.3 37.2 - - + -
360A VAL* 3.8 24.5 - - + -
361A LEU* 5.9 0.7 - - + -
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Residues in contact with TRP 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 ARG* 3.1 38.4 + - + +
303A ASP* 3.3 11.4 + - - +
305A ILE* 1.3 73.2 - - - +
307A ASN* 1.3 57.5 + - - +
309A LEU* 3.6 20.7 - - + +
310A ASN* 2.7 67.9 + - - +
360A VAL* 3.6 18.9 - - + +
363A GLU* 3.0 48.9 + - + -
364A GLN* 3.7 33.9 - - + -
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Residues in contact with ASN 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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303A ASP 3.0 18.0 + - - +
304A TYR* 3.4 23.6 - - - +
306A TRP* 1.3 78.7 - - - +
308A THR* 1.3 64.0 + - - +
310A ASN* 4.0 6.1 - - - +
311A SER* 3.0 36.1 + - - -
313A ARG* 4.7 8.7 + - - +
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Residues in contact with THR 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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284A TRP* 3.3 29.9 + - + +
304A TYR* 3.3 12.5 + - - -
305A ILE 3.2 8.7 + - - -
307A ASN* 1.3 80.1 + - - +
309A LEU* 1.3 64.8 - - - +
311A SER* 3.0 16.2 + - - -
313A ARG* 3.2 51.4 + - + +
314A VAL 3.6 22.7 - - - +
315A VAL* 4.4 7.6 - - + +
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Residues in contact with LEU 309 (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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305A ILE* 3.1 15.9 + - + +
306A TRP* 3.8 33.2 - - + +
308A THR* 1.3 78.8 - - - +
310A ASN* 1.3 63.9 + - - +
311A SER 3.0 1.4 + - - -
312A GLY* 3.0 14.2 + - - -
313A ARG 4.2 5.8 - - - +
315A VAL* 3.9 15.9 - - + -
360A VAL* 3.8 24.5 - - + -
361A LEU* 4.1 7.4 - - + -
364A GLN* 3.4 42.4 - - + +
700A ACO 3.6 24.9 - - + -
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Residues in contact with ASN 310 (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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306A TRP* 2.7 50.9 + - - +
307A ASN* 4.1 6.1 + - - +
309A LEU* 1.3 74.3 - - - +
311A SER* 1.3 59.0 + - - +
312A GLY 3.3 2.0 + - - -
364A GLN* 5.7 0.4 + - - -
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Residues in contact with SER 311 (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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307A ASN* 3.0 26.8 + - - -
308A THR 3.0 6.9 + - - -
310A ASN* 1.3 78.3 - - - +
312A GLY* 1.3 62.4 + - - +
313A ARG* 3.3 38.7 + - - -
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Residues in contact with GLY 312 (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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309A LEU 3.0 11.2 + - - -
310A ASN 3.3 2.2 + - - -
311A SER* 1.3 78.8 - - - +
313A ARG* 1.3 62.1 + - - +
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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