Contacts of the strand formed by residues 304 - 309 (chain C) in PDB entry 4ERQ
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 VAL 304 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C ILE* 3.7 6.8 - - - +
277C GLY* 3.3 30.9 - - - -
278C SER 3.2 11.8 + - - +
281C ASN 3.6 31.2 - - - +
282C LEU 3.7 15.5 - - - +
283C VAL* 4.1 3.8 - - + +
300C HIS* 3.7 24.7 - - + -
302C ASP 3.3 0.2 + - - -
303C VAL* 1.3 70.1 - - - +
305C ILE* 1.3 57.8 + - - +
306C SER 3.8 14.6 - - - +
307C THR* 4.1 7.0 - - + -
318C SER* 4.1 11.4 - - - -
319C ALA 3.5 12.8 - - - +
320C ALA* 4.4 0.2 - - - +
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Residues in contact with ILE 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C VAL 3.1 28.3 - - - +
49C SER* 3.6 12.6 - - - +
260C TYR* 3.6 33.0 - - + -
261C CYS 3.5 19.3 - - - +
262C ILE* 3.3 8.1 - - + -
263C PHE* 3.1 24.1 + - - -
303C VAL* 3.2 3.9 + - + -
304C VAL* 1.3 73.0 - - - +
306C SER* 1.3 62.9 + - - +
319C ALA* 3.0 14.8 + - + +
321C LEU* 3.7 20.9 - - + -
5340F ARG* 3.9 34.1 - - + +
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Residues in contact with SER 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C SER 3.8 3.1 - - - -
50C SER* 3.6 16.1 - - - -
51C VAL* 3.1 30.8 + - - +
263C PHE* 3.4 24.3 - - - +
304C VAL* 3.4 1.8 - - - +
305C ILE* 1.3 86.6 - - - +
307C THR* 1.3 69.9 + - - +
318C SER* 3.2 3.5 - - - -
319C ALA* 2.9 30.1 + - - +
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Residues in contact with THR 307 (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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51C VAL* 4.5 1.7 - - - +
52C LYS* 6.0 0.7 - - - -
263C PHE* 3.2 25.4 + - - +
265C ASN* 2.8 36.0 + - - +
275C VAL* 3.8 18.6 + - - +
276C SER* 3.8 6.0 - - - -
277C GLY 3.7 18.8 - - - +
283C VAL* 4.0 17.9 - - + -
304C VAL* 4.1 10.5 - - + -
306C SER* 1.3 83.3 + - - +
308C ALA* 1.3 61.3 + - - +
316C ILE* 4.7 1.8 - - + -
317C ALA 3.1 7.4 - - - -
318C SER* 4.2 6.5 - - - -
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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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51C VAL* 3.3 31.6 - - + +
52C LYS* 4.2 7.9 - - + -
53C PHE* 3.5 18.3 - - + +
265C ASN* 3.9 8.3 - - - +
307C THR* 1.3 76.2 - - - +
309C CYS* 1.3 64.8 + - - +
316C ILE* 3.3 8.4 - - - +
317C ALA* 2.8 30.5 + - + +
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Residues in contact with CYS 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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53C PHE* 3.5 9.6 - - - +
265C ASN* 3.8 29.1 - - + +
266C PHE 4.5 9.0 - - - +
267C SER* 3.9 31.4 - - - +
269C THR* 6.2 0.2 - - - +
275C VAL* 4.2 14.1 - - - -
308C ALA* 1.3 77.6 - - - +
310C HIS* 1.3 69.6 + - - +
311C PRO* 3.5 3.6 - - - +
315C ILE 3.6 4.5 - - - +
316C ILE* 4.3 9.4 - - - -
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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