Contacts of the helix formed by residues 302 - 311 (chain B) in PDB entry 5FV7
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 ASN 302 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B LEU* 2.7 22.0 + - + +
300B GLU 3.7 2.4 + - - +
301B PRO* 1.3 69.2 - - - +
303B GLU* 1.3 54.6 + - - +
304B GLU* 3.9 9.0 + - - +
305B GLU* 3.7 29.5 + - + +
306B LEU* 2.8 39.1 + - - +
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Residues in contact with GLU 303 (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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301B PRO 3.2 7.4 + - - +
302B ASN* 1.3 71.1 + - - +
304B GLU* 1.3 71.9 + - + +
306B LEU* 3.2 7.8 + - - +
307B ILE* 2.8 37.5 + - + +
322B ARG* 2.5 49.0 + - + +
325B VAL* 3.8 34.4 - - + +
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Residues in contact with GLU 304 (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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302B ASN* 3.4 8.2 + - - +
303B GLU* 1.3 91.4 - - + +
305B GLU* 1.3 58.2 + - - +
307B ILE* 3.0 9.2 + - - +
308B LYS* 2.9 29.2 + - - +
322B ARG* 3.9 16.9 + - - -
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Residues in contact with GLU 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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147B LEU* 3.5 23.2 - - + +
302B ASN* 3.4 29.8 + - - +
304B GLU* 1.3 77.6 - - - +
306B LEU* 1.3 57.3 + - - +
308B LYS* 3.9 7.5 - - - +
309B PHE* 3.1 29.1 + - - +
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Residues in contact with LEU 306 (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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68B PHE* 3.7 24.5 - - + -
144B LEU* 4.4 7.0 - - + -
147B LEU* 3.5 41.7 - - + +
148B MET* 4.0 10.8 - - + -
301B PRO* 4.0 10.1 - - + -
302B ASN 2.8 15.7 + - - +
303B GLU* 3.3 7.2 - - - +
305B GLU* 1.3 76.2 - - - +
307B ILE* 1.3 59.9 + - - +
309B PHE* 4.6 0.2 - - - -
310B MET* 2.9 61.6 + - + +
321B ILE* 4.2 9.4 - - + +
325B VAL* 3.8 21.5 - - + -
328B LEU* 5.2 0.4 - - + -
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Residues in contact with ILE 307 (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* 2.8 25.6 + - + +
304B GLU* 3.0 11.0 + - - +
306B LEU* 1.3 74.2 - - - +
308B LYS* 1.3 53.8 + - - +
309B PHE 3.0 5.4 + - - -
311B CYS* 3.1 29.8 + - + -
312B GLY* 2.7 32.2 + - - -
318B GLU* 3.8 21.8 - - + +
321B ILE* 3.8 14.8 - - + -
322B ARG* 3.5 43.1 - - + +
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Residues in contact with LYS 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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304B GLU 2.9 15.1 + - - +
305B GLU* 4.2 8.1 - - - +
307B ILE* 1.3 77.5 - - - +
309B PHE* 1.3 57.3 + - - +
312B GLY* 3.2 19.6 - - - -
313B GLU* 3.3 8.1 + - - +
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Residues in contact with PHE 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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64B LEU* 3.7 31.0 - - + -
140B GLU* 4.3 15.0 - - + -
143B HIS* 3.7 35.0 - + + -
144B LEU* 4.3 13.2 - - + -
147B LEU* 3.8 15.0 - - + -
305B GLU 3.1 17.5 + - - +
306B LEU 4.1 0.7 - - - +
307B ILE 3.0 1.8 - - - -
308B LYS* 1.3 78.4 - - - +
310B MET* 1.3 75.3 + - + +
311B CYS 3.5 0.2 - - - -
313B GLU* 3.1 10.7 + - + +
314B LYS* 2.9 52.1 + - + +
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Residues in contact with MET 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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64B LEU* 3.8 20.2 - - - +
65B MET* 5.0 0.7 - - - -
68B PHE* 3.8 28.0 - - + -
69B TYR* 6.2 0.9 - - + -
144B LEU* 3.8 16.6 - - + -
306B LEU* 2.9 40.5 + - + +
309B PHE* 1.3 85.0 - - + +
311B CYS* 1.3 57.3 + - - +
314B LYS* 3.1 9.6 - - - +
315B GLN 3.0 9.4 + - - -
316B PHE* 2.9 53.3 + - + -
321B ILE* 3.8 28.9 - - + -
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Residues in contact with CYS 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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307B ILE* 3.5 46.9 - - + -
310B MET* 1.3 74.8 - - - +
312B GLY* 1.3 65.4 + - - +
315B GLN* 3.8 11.2 - - - -
316B PHE 3.0 28.2 - - - +
318B GLU* 3.8 22.9 - - + +
321B ILE* 3.8 13.2 - - - -
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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