Contacts of the helix formed by residues 304 - 313 (chain A) in PDB entry 1EQR
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 PHE 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A VAL* 3.3 9.4 - - + +
303A GLU* 1.3 79.1 - - - +
305A ALA* 1.3 67.0 + - - +
306A VAL* 3.3 38.9 + - + -
307A PHE* 3.3 32.3 + + + -
308A ALA* 3.1 24.5 + - - +
350A ALA* 5.2 1.3 - - + -
368A VAL* 3.8 27.1 - - + -
371A PHE* 3.7 54.1 - + + -
372A LEU* 5.6 0.2 - - + -
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLU 3.0 7.7 + - - +
304A PHE* 1.3 75.1 - - - +
306A VAL* 1.3 64.0 + - + +
308A ALA* 4.6 5.2 - - - -
309A GLY* 3.2 21.8 + - - +
310A PRO* 3.9 1.9 - - - +
347A LYS* 4.8 1.0 + - - -
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 3.3 31.9 - - + -
305A ALA* 1.3 77.9 - - + +
307A PHE* 1.3 71.3 + - + +
310A PRO* 3.2 19.3 - - - +
347A LYS* 3.4 39.3 + - + +
350A ALA* 5.7 3.6 - - + -
396A ALA* 3.2 9.0 - - + +
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.6 37.7 - - + -
302A VAL* 4.0 11.0 - - + -
304A PHE* 3.3 25.6 + + - +
305A ALA 3.2 0.4 - - - -
306A VAL* 1.3 89.2 - - + +
308A ALA* 1.3 69.9 + - - +
309A GLY 2.9 3.0 + - - -
310A PRO* 2.9 8.7 - - - +
311A ALA* 2.9 24.2 + - - +
318A VAL* 4.2 8.9 - - + +
350A ALA* 3.9 30.1 - - + -
368A VAL* 4.6 5.8 - - + -
372A LEU* 4.0 27.4 - - + -
380A ILE* 6.0 0.4 - - + -
394A PHE* 4.2 26.2 - + + -
396A ALA* 4.0 9.4 - - + -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU 3.5 14.8 + - - +
300A LYS 4.4 1.8 - - - +
302A VAL* 3.5 25.8 - - + +
303A GLU 4.8 1.1 - - - +
304A PHE 3.1 17.3 + - - +
305A ALA* 4.6 2.5 - - - -
307A PHE* 1.3 77.8 - - - +
309A GLY* 1.3 66.0 + - - +
311A ALA* 3.1 0.6 + - - -
312A ASN* 2.6 38.7 + - - +
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Residues in contact with GLY 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 ALA* 3.2 12.9 + - - +
307A PHE 2.9 2.4 + - - -
308A ALA* 1.3 83.6 - - - +
310A PRO* 1.3 66.4 - - - +
312A ASN* 2.9 11.7 + - - +
313A ASP* 3.1 12.7 + - - +
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Residues in contact with PRO 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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305A ALA 3.9 1.8 - - - +
306A VAL 3.2 25.8 - - - +
307A PHE 2.9 18.6 - - - +
309A GLY* 1.3 78.9 - - - +
311A ALA* 1.3 58.0 + - - -
312A ASN 3.3 0.4 - - - -
313A ASP* 3.6 14.5 - - + +
316A GLY* 3.4 26.9 - - - -
317A ARG 3.7 1.7 + - - +
318A VAL* 4.0 5.6 - - + -
347A LYS* 4.6 6.1 - - - +
396A ALA* 3.5 17.9 - - + +
397A ASP* 3.4 33.0 - - - +
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Residues in contact with ALA 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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296A ALA* 3.5 43.5 - - + +
299A LEU* 3.8 17.0 - - + +
300A LYS* 2.5 33.9 + - - +
307A PHE 2.9 17.2 + - - +
308A ALA 3.6 4.0 - - - +
310A PRO* 1.3 78.8 - - - +
312A ASN* 1.3 52.8 + - - +
313A ASP 3.4 2.8 - - - +
316A GLY 5.6 0.2 - - - -
318A VAL* 4.4 3.4 - - + -
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Residues in contact with ASN 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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300A LYS* 3.3 54.0 + - - +
308A ALA* 2.6 33.0 + - - +
309A GLY* 3.7 3.6 - - - +
311A ALA* 1.3 77.0 - - - +
313A ASP* 1.3 61.7 + - - +
314A PRO* 3.7 7.8 - - - +
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Residues in contact with ASP 313 (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 LYS* 5.7 0.2 + - - -
309A GLY 3.1 13.0 + - - +
310A PRO* 3.6 17.6 - - + +
311A ALA 3.4 2.6 - - - +
312A ASN* 1.3 79.1 + - - +
314A PRO* 1.3 79.6 - - - +
315A LYS* 2.9 28.6 + - - +
316A GLY* 3.0 25.0 + - - +
397A ASP 4.9 0.9 - - - +
398A ASN* 4.9 7.3 - - - +
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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