Contacts of the helix formed by residues 300 - 308 (chain B) in PDB entry 5I94
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 GLY 300 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B VAL* 2.9 22.0 + - - -
297B ASN 4.7 0.4 + - - -
298B ASP 3.9 0.6 - - - -
299B LEU* 1.3 83.8 - - - +
301B THR* 1.3 67.7 + - - +
302B GLU 3.4 3.3 + - - -
303B TYR 3.6 0.4 + - - -
304B VAL* 3.4 19.2 + - - +
450B GLU* 3.8 8.3 - - - -
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Residues in contact with THR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A PHE* 4.1 19.3 - - + -
474A HIS* 4.9 9.0 - - + -
296B VAL* 4.0 3.7 - - - +
300B GLY* 1.3 72.7 - - - +
302B GLU* 1.3 67.1 + - - +
305B HIS* 3.1 33.4 + - + +
310B LYS* 5.3 1.6 - - - +
450B GLU* 2.8 34.2 + - - +
454B ASN* 2.7 33.9 + - - +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLY 3.4 0.4 - - - -
301B THR* 1.3 82.8 - - - +
303B TYR* 1.3 68.5 + - - +
305B HIS* 3.5 4.5 + - - +
306B ARG* 3.2 51.8 + - - +
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Residues in contact with TYR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 3.5 57.6 + - + +
300B GLY 3.6 1.4 + - - -
301B THR 3.4 0.4 - - - -
302B GLU* 1.3 83.1 + - - +
304B VAL* 1.3 81.1 + - - +
306B ARG* 2.7 51.6 + - - +
307B TYR* 3.6 34.3 + + - -
343B LEU* 4.1 12.9 - - + +
346B GLN* 2.9 25.6 + - - -
401B PRO* 4.5 1.7 - - - +
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TYR* 4.0 26.0 - - + -
295B ALA* 3.7 38.6 - - + +
296B VAL* 3.9 4.7 - - + +
299B LEU* 4.0 8.5 - - + -
300B GLY 3.4 17.3 + - - +
301B THR 4.1 2.5 - - - +
303B TYR* 1.3 80.9 - - + +
305B HIS* 1.3 61.1 + - + +
307B TYR* 3.0 23.7 + - - +
308B VAL* 3.5 23.8 + - + +
340B VAL* 5.1 1.1 - - + -
343B LEU* 4.3 18.1 - - + +
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Residues in contact with HIS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A PHE* 3.8 7.4 - + - -
292B TYR* 2.7 37.9 + + - -
296B VAL* 4.9 0.2 - - + -
301B THR* 3.1 38.8 + - + +
302B GLU* 3.7 4.5 - - - +
303B TYR 3.1 1.2 - - - -
304B VAL* 1.3 80.6 - - + +
306B ARG* 1.3 60.3 + - - +
307B TYR 3.1 1.1 + - - -
308B VAL* 2.8 27.3 + - + +
309B GLY 3.1 21.6 + - - -
310B LYS* 3.9 35.6 - - + +
327B LYS* 3.0 21.7 + - - -
331B PRO* 4.6 0.4 - - + -
454B ASN* 4.9 0.2 - - - -
458B LEU* 4.4 3.4 - - + -
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Residues in contact with ARG 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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302B GLU* 3.2 39.6 + - - +
303B TYR* 2.7 51.4 + - - +
305B HIS* 1.3 71.7 - - - +
307B TYR* 1.3 68.9 + - + +
327B LYS* 3.2 22.8 - - - +
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Residues in contact with TYR 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 TYR* 3.6 44.8 + + - -
304B VAL 3.0 8.2 + - - +
306B ARG* 1.3 96.7 - - + +
308B VAL* 1.3 58.5 + - + +
327B LYS* 3.7 8.7 - - - +
328B PRO* 3.3 21.1 - - - +
339B VAL* 3.7 19.4 - - + +
343B LEU* 3.9 18.6 - - + -
399B CYS* 3.5 21.3 - - - +
400B PHE 3.9 4.0 - - - -
401B PRO* 3.7 41.7 - - + +
402B GLU 5.0 0.5 + - - -
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B VAL* 3.6 29.8 - - + +
305B HIS* 2.8 40.1 + - - +
306B ARG 3.7 0.6 - - - -
307B TYR* 1.3 82.6 - - + +
309B GLY* 1.3 58.8 + - - +
327B LYS* 3.8 6.4 - - - +
328B PRO* 3.9 10.5 - - + +
330B ASN* 3.5 31.9 - - - +
331B PRO* 3.7 13.5 - - + -
336B GLY* 4.0 19.5 - - - +
339B VAL* 4.9 4.3 - - + -
340B VAL* 4.4 7.6 - - + -
343B LEU* 5.6 0.7 - - + -
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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