Contacts of the helix formed by residues 304 - 313 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A VAL* 3.6 7.4 - - + -
183A HIS* 3.7 21.5 + + - +
559B ALA* 3.9 24.5 - - + -
302C VAL* 3.1 11.5 - - + +
303C GLU* 1.3 73.9 - - - +
305C ALA* 1.3 65.4 + - - +
306C VAL* 3.1 41.7 - - + -
307C PHE* 3.0 30.4 + + - -
308C ALA* 2.8 24.8 + - - +
368C VAL* 4.1 18.2 - - + -
371C PHE* 3.7 45.3 + + + +
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Residues in contact with ALA 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ARG 3.5 20.6 - - - +
182A VAL* 2.7 24.6 + - + +
184A LYS* 3.9 17.9 - - - +
303C GLU 2.9 5.4 + - - +
304C PHE* 1.3 70.9 - - - +
306C VAL* 1.3 59.3 + - + +
308C ALA* 4.1 8.5 - - - -
309C GLY* 2.9 27.8 + - - +
310C PRO* 3.6 1.9 - - - +
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Residues in contact with VAL 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 4.2 12.3 - - + -
220B ASP* 4.8 12.8 - - - +
221B LEU* 6.1 1.6 - - + -
559B ALA* 5.8 2.2 - - + -
304C PHE* 3.0 38.5 + - + -
305C ALA* 1.3 75.6 - - + +
307C PHE* 1.3 65.3 + - + +
310C PRO* 3.2 19.5 - - - +
396C ALA* 3.5 14.8 - - + +
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Residues in contact with PHE 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C LEU* 4.2 24.5 - - + -
302C VAL* 4.1 9.4 - - + -
304C PHE* 3.0 23.9 + + - +
306C VAL* 1.3 88.1 - - + +
308C ALA* 1.3 66.8 + - - +
309C GLY 3.4 0.2 - - - -
310C PRO* 3.1 8.1 - - - +
311C ALA* 3.0 23.2 + - - +
318C VAL* 3.5 13.3 - - + +
350C ALA* 4.0 23.8 - - + -
368C VAL* 4.1 16.4 - - + -
372C LEU* 3.6 33.2 - - + -
394C PHE* 4.1 30.5 - + + -
396C ALA* 4.0 16.4 - - + -
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Residues in contact with ALA 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LYS* 6.2 2.7 - - + -
299C LEU 4.1 11.4 - - - +
300C LYS 4.6 1.3 - - - +
302C VAL* 3.2 28.9 - - + +
303C GLU 4.9 0.7 - - - -
304C PHE 2.8 15.1 + - - +
305C ALA* 4.1 3.4 - - - -
307C PHE* 1.3 75.1 - - - +
309C GLY* 1.3 70.3 + - - +
311C ALA* 3.1 1.2 + - - -
312C ASN* 3.0 35.7 + - - +
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Residues in contact with GLY 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LYS* 6.2 2.7 - - - -
305C ALA* 2.9 21.4 + - - +
308C ALA* 1.3 76.5 - - - +
310C PRO* 1.3 60.0 - - - +
312C ASN* 3.3 3.0 + - - +
313C ASP* 3.0 26.9 + - - +
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Residues in contact with PRO 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C ALA* 5.2 0.2 - - - +
305C ALA 3.6 3.8 - - - +
306C VAL 3.2 21.5 - - - +
307C PHE 3.1 15.5 - - - +
309C GLY* 1.3 87.2 - - - +
311C ALA* 1.3 61.4 + - - -
312C ASN 3.3 0.2 - - - -
313C ASP* 3.4 22.9 - - + +
316C GLY* 3.5 1.1 - - - +
317C ARG* 3.3 23.0 + - - +
318C VAL* 4.3 1.8 - - + -
396C ALA* 3.8 16.2 - - + +
397C ASP* 3.8 31.0 - - - +
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Residues in contact with ALA 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C ALA* 3.6 36.9 - - - +
299C LEU* 4.2 4.3 - - + -
300C LYS* 3.7 34.1 + - - +
307C PHE 3.0 18.6 + - - +
308C ALA 3.1 3.8 + - - +
310C PRO* 1.3 78.6 - - - +
312C ASN* 1.3 60.4 + - - +
313C ASP 4.9 1.0 - - - -
318C VAL* 3.7 13.4 - - + +
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Residues in contact with ASN 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B GLU* 5.6 2.4 - - - +
300C LYS* 2.7 57.5 + - - +
308C ALA* 3.0 29.0 + - - +
309C GLY* 3.9 2.7 - - - +
311C ALA* 1.3 76.9 - - - +
313C ASP* 1.3 59.9 + - - +
314C PRO* 3.0 17.2 - - - +
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Residues in contact with ASP 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C GLY 3.0 18.4 + - - +
310C PRO* 3.4 12.7 + - + +
311C ALA 3.3 2.3 - - - +
312C ASN* 1.3 76.4 - - - +
314C PRO* 1.3 55.3 - - - +
315C LYS* 2.8 22.0 + - - +
316C GLY* 2.6 47.8 + - - +
397C ASP 5.7 0.3 - - - -
398C ASN* 5.1 4.2 - - - +
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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