Contacts of the helix formed by residues 304 - 313 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B VAL* 3.3 11.0 - - + +
303B GLU* 1.3 75.1 - - - +
305B ALA* 1.3 64.3 + - - +
306B VAL* 3.6 35.9 - - + -
307B PHE* 3.2 31.4 + + + -
308B ALA* 2.8 27.3 + - - +
350B ALA* 5.7 0.4 - - + -
368B VAL* 3.8 25.6 - - + -
371B PHE* 3.6 53.0 + + + +
372B LEU* 5.5 0.4 - - + -
221C LEU* 5.6 1.6 - - + -
559C ALA* 4.1 17.9 - - + -
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B GLU 3.1 9.0 + - - +
304B PHE* 1.3 70.6 - - - +
306B VAL* 1.3 69.2 + - + +
307B PHE 2.9 1.4 + - - -
308B ALA* 4.3 6.5 - - - -
309B GLY* 3.0 21.5 + - - +
310B PRO* 3.4 4.3 - - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PHE* 3.3 36.5 - - + -
305B ALA* 1.3 78.2 - - + +
307B PHE* 1.3 69.6 + - + +
310B PRO* 3.1 22.5 - - - +
350B ALA* 6.2 1.3 - - + -
396B ALA* 3.5 15.4 - - + +
221C LEU* 4.0 25.1 - - + -
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Residues in contact with PHE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 4.0 25.1 - - + -
302B VAL* 4.3 8.5 - - + -
304B PHE* 3.2 24.9 + + + +
305B ALA 3.0 0.2 - - - -
306B VAL* 1.3 89.1 - - + +
308B ALA* 1.3 57.1 + - - +
309B GLY 3.1 2.3 + - - -
310B PRO* 3.2 2.3 - - - +
311B ALA* 2.8 38.3 + - - +
318B VAL* 4.0 7.8 - - + +
350B ALA* 3.9 26.9 - - + -
368B VAL* 4.1 14.1 - - + -
372B LEU* 3.8 30.5 - - + -
394B PHE* 4.1 28.0 - + + -
396B ALA* 3.7 26.0 - - + -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B LEU 3.9 13.5 - - - +
300B LYS 4.7 1.8 - - - +
302B VAL* 3.4 25.2 - - + +
303B GLU 4.8 1.3 - - - +
304B PHE 2.8 25.3 + - - +
305B ALA* 4.3 3.1 - - - -
307B PHE* 1.3 72.7 - - - +
309B GLY* 1.3 56.2 + - - +
311B ALA* 3.7 0.2 - - - +
312B ASN* 2.9 42.2 + - - +
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Residues in contact with GLY 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ALA* 3.0 14.6 + - - +
308B ALA* 1.3 73.1 - - - +
310B PRO* 1.3 56.3 - - - +
311B ALA 3.0 1.1 - - - -
312B ASN* 2.8 8.6 + - - +
313B ASP* 2.6 36.5 + - - +
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Residues in contact with PRO 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ALA 3.4 4.7 - - - +
306B VAL 3.1 27.1 - - - +
307B PHE 3.2 4.0 - - - +
309B GLY* 1.3 90.6 - - - +
311B ALA* 1.3 60.5 + - - +
313B ASP* 3.6 11.0 - - + +
316B GLY* 3.2 29.3 - - - +
317B ARG* 3.6 4.8 + - - +
318B VAL* 4.2 3.8 - - + -
347B LYS* 5.9 2.0 - - - +
396B ALA 3.3 30.3 - - - +
397B ASP* 3.8 15.7 - - - +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B ALA* 3.7 37.2 - - - +
299B LEU* 4.2 12.6 - - + +
300B LYS* 3.4 21.4 + - - +
307B PHE 2.8 23.4 + - - +
308B ALA 3.7 4.5 - - - +
310B PRO* 1.3 80.5 - - - +
312B ASN* 1.3 60.9 + - - +
313B ASP 4.0 3.3 - - - +
316B GLY 5.1 0.9 - - - +
318B VAL* 3.9 10.5 - - + +
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Residues in contact with ASN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B LYS* 2.7 57.8 + - - +
308B ALA* 2.9 27.1 + - - +
309B GLY* 2.8 5.6 + - - +
311B ALA* 1.3 76.7 - - - +
313B ASP* 1.3 65.5 + - - +
314B PRO* 3.3 5.2 - - - +
586C LYS* 6.4 0.9 - - - -
588C GLU* 3.7 22.9 - - - +
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B GLY 2.6 20.0 + - - +
310B PRO* 3.6 8.9 - - + +
311B ALA 3.5 3.1 - - - +
312B ASN* 1.3 74.4 - - - +
314B PRO* 1.3 77.8 - - - +
315B LYS* 2.7 52.8 + - - +
316B GLY* 3.4 24.9 + - - +
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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