Contacts of the strand formed by residues 295 - 300 (chain B) in PDB entry 3SMP
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 LEU 295 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293B LEU 3.8 5.2 - - - +
294B GLU* 1.3 70.8 - - - +
296B LYS* 1.3 61.1 + - - +
298B LEU* 3.5 28.5 - - + +
306B ASN* 3.2 8.1 - - - +
307B LEU* 2.9 39.1 + - + +
309B PHE* 4.0 20.2 - - + -
374B VAL* 4.1 21.1 - - + -
377B VAL* 4.1 14.4 - - + -
378B GLY 3.7 15.7 - - - +
379B PHE* 3.6 32.1 - - + -
380B ASN* 3.5 2.9 - - - +
578B HIS* 3.6 11.9 - - + +
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Residues in contact with LYS 296 (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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291B VAL 5.8 0.9 - - - -
294B GLU* 3.9 24.4 + - - +
295B LEU* 1.3 77.6 - - - +
297B ASN* 1.3 73.0 + - + +
298B LEU* 3.5 3.1 + - - +
306B ASN* 3.5 20.6 - - - +
380B ASN* 2.7 35.1 + - - +
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Residues in contact with ASN 297 (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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296B LYS* 1.3 77.4 - - + +
298B LEU* 1.3 61.5 + - - +
304B LYS* 5.1 12.6 - - - +
305B GLY 3.2 6.5 + - - +
306B ASN* 2.9 14.6 + - - -
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Residues in contact with LEU 298 (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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253B PHE* 3.8 24.9 - - + -
295B LEU* 3.5 39.0 - - + +
296B LYS 4.6 2.0 - - - +
297B ASN* 1.3 76.7 - - - +
299B THR* 1.3 62.9 + - - +
300B MET* 4.5 2.0 - - + -
304B LYS* 3.3 6.6 - - - +
305B GLY 2.9 44.4 + - - +
307B LEU* 4.2 11.4 - - + +
373B TYR* 3.5 22.0 - - + +
377B VAL* 3.8 34.1 - - + +
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Residues in contact with THR 299 (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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298B LEU* 1.3 76.4 + - - +
300B MET* 1.3 60.1 + - - +
301B CYS 4.6 0.2 - - - +
302B GLY* 3.7 29.4 - - - +
303B ARG 3.3 9.0 + - - +
304B LYS* 4.6 9.4 - - + +
373B TYR* 2.7 27.8 + - - -
377B VAL* 4.6 5.1 - - - +
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Residues in contact with MET 300 (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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238B TRP* 3.4 18.6 - - + -
253B PHE* 3.7 25.1 - - + -
298B LEU* 4.2 2.0 - - + -
299B THR* 1.3 71.8 - - - +
301B CYS* 1.3 71.5 + - - +
302B GLY 3.1 0.7 - - - -
303B ARG 2.9 17.9 + - - +
307B LEU* 4.2 26.0 - - + -
373B TYR* 3.1 37.9 - - + +
585B VAL* 5.8 1.3 - - + -
588B LEU* 4.2 8.3 - - + -
589B LEU* 3.5 29.6 - - + -
592B PHE* 3.6 27.4 - - + -
3599B CL 3.9 2.7 - - - -
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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