Contacts of the helix formed by residues 299 - 308 (chain B) in PDB entry 5J3V
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 LYS 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259B GLU* 5.6 7.3 + - - +
262B LEU* 4.0 25.0 - - + +
296B HIS* 5.3 6.5 - - - +
297B LEU* 3.0 1.2 - - - +
298B PRO* 1.3 86.3 - - + +
300B LEU* 1.3 62.7 + - - +
301B ILE 3.4 1.3 - - - -
302B PRO* 3.5 10.0 - - - +
303B VAL* 3.2 26.7 - - - +
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU* 3.8 12.7 - - + +
280B TRP* 3.5 48.0 - - + +
293B LEU* 3.7 40.8 - - + -
296B HIS 3.2 19.8 + - - +
297B LEU* 3.1 8.1 + - + +
299B LYS* 1.3 78.7 - - - +
301B ILE* 1.3 61.2 + - + +
303B VAL* 3.4 4.8 + - + +
304B LEU* 3.1 38.5 + - + +
386B LEU* 4.1 16.4 - - + -
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 3.3 17.2 + - + +
298B PRO* 5.4 0.4 - - + -
300B LEU* 1.3 75.4 - - + +
302B PRO* 1.4 67.9 - - + +
303B VAL 3.1 1.8 - - - -
304B LEU* 3.1 9.6 + - + +
305B VAL* 2.8 45.3 + - + +
383B LEU* 4.6 9.2 - - + -
386B LEU* 5.8 4.0 - - + -
394B LEU* 3.6 28.5 - - + -
397B HIS* 3.6 37.9 - - + +
398B ILE* 3.7 28.5 - - + -
401B LEU* 4.8 3.1 - - + -
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Residues in contact with PRO 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PRO 3.3 26.9 - - - +
299B LYS* 3.5 12.6 - - - +
301B ILE* 1.4 94.0 - - + +
303B VAL* 1.3 58.0 + - + +
305B VAL* 3.9 9.0 - - + +
306B ASN* 3.2 27.0 + - - +
397B HIS 5.6 0.7 - - - +
401B LEU* 3.9 24.2 - - + -
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU* 4.3 14.6 - - + +
265B THR* 3.2 33.7 - - + +
266B GLN* 3.7 37.8 - - + +
299B LYS* 3.2 16.4 - - + +
300B LEU* 3.4 12.8 + - + +
301B ILE 3.1 0.4 - - - -
302B PRO* 1.3 78.4 - - + +
304B LEU* 1.3 68.8 + - + +
306B ASN* 3.5 6.2 + - - +
307B GLY* 3.1 18.5 + - - -
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B THR* 5.8 0.7 - - + -
277B CYS* 3.9 17.9 - - - -
280B TRP* 3.8 27.8 - - + +
300B LEU* 3.1 32.7 + - + +
301B ILE* 3.7 6.5 - - + +
303B VAL* 1.3 77.2 - - + +
305B VAL* 1.3 65.8 + - - +
307B GLY* 3.1 2.5 + - - +
308B MET* 3.1 30.6 + - + +
379B SER* 3.6 15.9 - - - +
382B ALA* 4.2 17.7 - - + -
383B LEU* 4.6 14.6 - - + +
386B LEU* 4.0 26.7 - - + -
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 2.8 35.2 + - + +
302B PRO* 3.9 8.1 - - + +
304B LEU* 1.3 76.8 - - - +
306B ASN* 1.3 63.2 + - - +
308B MET* 3.2 25.8 + - + +
309B LYS* 3.8 5.0 + - - +
383B LEU* 5.1 3.6 - - + -
398B ILE* 5.6 3.6 - - + -
401B LEU* 5.1 10.3 - - + -
405B LEU* 3.7 35.7 - - + -
416B SER* 4.8 6.4 - - - +
420B VAL* 4.2 22.4 - - + +
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Residues in contact with ASN 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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266B GLN* 5.7 9.2 - - - +
302B PRO 3.2 16.7 + - - +
303B VAL* 3.8 5.6 + - - +
304B LEU 3.3 0.2 - - - -
305B VAL* 1.3 80.6 - - - +
307B GLY* 1.3 60.5 + - - +
309B LYS* 3.4 44.5 + - - +
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Residues in contact with GLY 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 VAL 3.1 14.0 + - - -
304B LEU 3.1 5.1 + - - -
305B VAL 3.1 0.6 - - - -
306B ASN* 1.3 76.2 - - - +
308B MET* 1.3 58.0 - - - +
309B LYS 3.1 12.5 + - - +
375B LEU* 3.8 19.0 - - - +
376B ARG* 3.5 17.8 + - - -
379B SER* 3.8 13.5 - - - -
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Residues in contact with MET 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 LEU 3.1 25.9 + - - +
305B VAL* 3.2 22.3 + - + +
307B GLY* 1.3 74.4 - - - +
309B LYS* 1.3 62.2 + - - +
310B TYR 3.7 0.2 + - - -
376B ARG* 3.3 32.1 + - - +
379B SER* 3.7 5.6 - - - +
380B ALA* 3.5 43.5 - - + +
383B LEU* 3.6 38.1 - - + -
415B GLU* 4.8 0.3 - - - +
416B SER* 4.2 9.2 - - - -
419B LEU* 3.9 19.6 - - + +
420B VAL* 3.7 15.9 - - + -
423B ALA* 4.9 1.1 - - - -
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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