Contacts of the helix formed by residues 296 - 309 (chain A) in PDB entry 5ID6
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 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A THR* 1.3 87.7 - - - +
297A ASP* 1.3 59.6 + - - +
298A GLU* 3.6 9.3 + - - +
299A GLU* 3.0 25.7 + - - +
300A VAL* 2.9 29.5 + - - +
510A TYR* 3.3 12.0 + - - -
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Residues in contact with ASP 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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296A SER* 1.3 72.0 - - - +
298A GLU* 1.3 61.9 + - - +
300A VAL* 4.0 1.1 - - - +
301A LEU* 3.0 30.3 + - - +
442A LEU* 3.6 20.2 - - + +
445A SER* 3.0 16.3 + - - -
446A LEU* 2.7 53.8 + - - +
510A TYR* 2.8 21.2 + - - -
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Residues in contact with GLU 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 SER* 3.1 8.3 + - - +
297A ASP* 1.3 79.0 - - - +
299A GLU* 1.3 58.5 + - - +
301A LEU* 4.0 7.0 - - - +
302A GLU* 3.1 30.0 + - + +
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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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292A GLU* 5.2 5.0 - - - +
293A GLY* 3.3 27.3 + - - +
295A THR* 3.0 40.4 + - + +
296A SER* 3.0 19.9 + - - +
298A GLU* 1.3 74.2 - - - +
300A VAL* 1.3 66.8 + - - +
301A LEU 3.1 1.6 - - - -
302A GLU* 3.0 19.8 + - - +
303A VAL* 3.0 19.9 + - + +
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLY* 4.5 9.2 - - - -
294A TYR 3.6 20.6 - - - +
296A SER 2.9 22.3 + - - +
297A ASP 4.0 3.6 - - - +
299A GLU* 1.3 71.4 - - - +
301A LEU* 1.3 63.2 + - - +
303A VAL* 3.5 3.6 + - - +
304A PHE* 3.3 20.4 + - - +
446A LEU* 3.8 21.3 - - + -
456A MSE 4.5 8.1 - - - -
507A ILE* 4.3 31.8 - - + +
510A TYR* 3.6 32.8 - - + -
511A VAL* 6.1 0.7 - - + -
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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
----------------------------------------------------------
297A ASP 3.0 15.8 + - - +
298A GLU* 4.0 9.2 - - - +
300A VAL* 1.3 76.8 - - - +
302A GLU* 1.3 65.3 + - - +
304A PHE* 3.3 2.5 + - + +
305A ARG* 3.0 55.8 + - + +
435A LEU* 4.9 2.0 - - + +
440A PHE* 3.7 31.6 - - + +
442A LEU* 4.0 33.2 - - + +
446A LEU* 4.4 9.2 - - + -
452A VAL* 4.8 4.7 - - + -
456A MSE 3.6 25.6 - - + -
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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 GLU* 3.1 25.3 + - + +
299A GLU* 3.0 10.7 + - - +
301A LEU* 1.3 75.3 - - - +
303A VAL* 1.3 70.8 + - - +
305A ARG* 3.9 8.0 - - - +
306A ASN* 2.9 55.3 + - - +
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Residues in contact with VAL 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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292A GLU 3.8 33.4 - - - +
293A GLY* 4.3 5.2 - - - +
299A GLU* 3.0 19.3 + - + +
300A VAL 3.9 6.5 - - - +
302A GLU* 1.3 86.4 - - - +
304A PHE* 1.3 60.0 + - - +
306A ASN* 3.1 3.1 + - - -
307A THR* 2.8 41.6 + - + +
503A ILE* 3.6 35.0 - - + -
507A ILE* 5.3 1.1 - - + -
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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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300A VAL 3.3 7.3 + - - +
301A LEU* 3.3 8.2 + - + +
303A VAL* 1.3 78.2 - - - +
305A ARG* 1.3 67.9 + - + +
307A THR* 4.2 4.0 - - - -
308A LEU* 3.1 48.8 + - + +
432A SER* 5.5 0.9 - - - -
435A LEU* 3.8 26.0 - - + -
436A PHE* 3.4 32.6 - + - -
455A ILE 4.8 0.7 - - - -
456A MSE 3.6 66.2 - - + -
459A LEU* 4.2 15.9 - - + -
460A LEU* 4.4 2.5 - - + -
507A ILE* 4.3 18.1 - - + +
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Residues in contact with ARG 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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301A LEU* 3.0 43.0 + - + +
302A GLU* 3.9 7.3 - - - +
304A PHE* 1.3 80.6 - - + +
306A ASN* 1.3 58.4 + - - +
309A ASN* 2.8 40.5 + - - +
435A LEU 2.8 38.5 + - - +
436A PHE* 3.8 15.9 + - + -
437A ASP 2.7 32.9 + - - -
438A ALA* 3.4 23.2 + - - +
440A PHE* 3.6 16.9 + - - +
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Residues in contact with ASN 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* 2.9 49.2 + - - +
303A VAL* 3.1 4.9 + - - +
305A ARG* 1.3 84.3 - - - +
307A THR* 1.3 65.2 + - + +
309A ASN* 3.5 14.0 + - - +
312A SER* 3.8 6.6 - - - -
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Residues in contact with THR 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 VAL* 2.8 30.8 + - + +
304A PHE* 3.9 0.7 + - - -
306A ASN* 1.3 80.1 - - + +
308A LEU* 1.3 80.9 + - - +
312A SER* 2.9 19.1 + - - -
313A GLU* 5.9 0.2 - - - +
314A ILE* 3.7 21.0 - - + +
503A ILE* 3.9 30.3 - - + +
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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
----------------------------------------------------------
304A PHE* 3.1 25.2 + - + +
307A THR* 1.3 96.3 - - - +
309A ASN* 1.3 62.7 + - - +
312A SER* 3.6 1.6 - - - -
314A ILE* 3.8 28.0 - - + -
429A TYR* 2.5 43.5 + - - +
436A PHE* 3.4 8.3 - - + -
459A LEU* 3.9 22.0 - - + -
460A LEU* 3.5 31.6 - - + -
463A VAL* 5.1 7.6 - - + -
500A VAL* 4.7 7.2 - - + -
503A ILE* 4.7 6.3 - - + -
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Residues in contact with ASN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ARG 2.8 27.9 + - - +
306A ASN* 3.5 15.8 + - - +
308A LEU* 1.3 80.7 - - - +
310A LYS* 1.3 58.3 + - - +
311A ASN* 2.8 40.4 + - - +
312A SER* 2.8 32.3 + - - +
315A PHE* 3.6 3.5 - - - +
429A TYR* 4.4 0.2 - - - -
436A PHE* 3.4 28.2 - - + +
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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