Contacts of the strand formed by residues 290 - 294 (chain B) in PDB entry 5C16
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 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B TRP* 5.7 0.9 - - - -
261B TYR* 3.9 13.7 - - + +
265B ILE* 4.0 24.5 - - + -
266B VAL 3.7 9.0 - - - +
267B VAL* 4.0 10.3 - - + -
288B VAL* 3.6 25.4 - - + +
289B PRO* 1.3 80.0 - - - +
291B LEU* 1.3 62.8 + - - +
292B SER 3.4 0.3 + - - -
303B THR* 3.1 7.4 - - - -
304B ARG* 2.9 31.1 + - + +
477B PHE* 3.5 38.4 - - + -
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B TYR* 4.1 24.6 + - + -
239B GLN* 3.9 5.6 - - - +
241B LEU* 3.5 35.2 - - + -
246B TRP* 3.6 35.6 - - + -
266B VAL* 3.0 26.0 + - + +
290B VAL* 1.3 73.1 - - - +
292B SER* 1.3 65.6 + - - +
293B TRP 3.6 22.0 - - - +
294B ILE* 4.2 4.7 - - + -
301B THR* 3.8 19.3 - - + -
302B ILE 3.8 5.4 - - - +
303B THR* 4.0 4.4 - - - +
472B LYS* 4.5 0.9 + - - -
477B PHE* 4.7 8.2 - - - -
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Residues in contact with SER 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLN* 3.3 10.7 + - - -
290B VAL 3.4 1.6 + - - -
291B LEU* 1.3 76.7 - - - +
293B TRP* 1.3 59.2 + - - +
302B ILE* 2.8 26.9 + - - -
304B ARG* 3.3 23.7 - - - +
449B THR* 4.4 2.2 - - - -
453B MET* 3.9 13.4 - - - +
472B LYS* 2.7 27.4 + - - +
473B GLU* 3.1 29.2 + - - -
477B PHE* 5.2 0.8 - - - -
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Residues in contact with TRP 293 (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 ARG* 4.3 0.8 - - - +
239B GLN* 3.2 25.8 - - - +
291B LEU* 3.6 4.7 - - - +
292B SER* 1.3 79.6 - - - +
294B ILE* 1.3 76.6 + - - +
295B HIS* 3.7 31.6 - + + -
296B PRO* 4.0 11.7 - - + -
300B ALA 4.6 1.6 - - - -
301B THR* 3.3 5.5 - - - +
302B ILE* 2.8 38.0 + - + +
427B ILE* 3.7 27.6 - - + -
453B MET* 4.0 17.5 - - + -
456B LEU* 3.8 35.7 - - + -
457B ASP* 2.9 40.4 + - + +
460B TYR* 3.8 20.9 - + - -
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Residues in contact with ILE 294 (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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239B GLN* 3.0 37.9 + - - +
240B GLY 5.5 0.2 - - - -
241B LEU* 3.8 19.1 - - + -
243B ASN* 3.9 13.7 - - - +
246B TRP* 4.0 14.1 - - + +
291B LEU* 4.2 3.4 - - + -
293B TRP* 1.3 94.2 + - - +
295B HIS* 1.3 74.1 + - - +
296B PRO* 3.6 5.2 - - + +
299B GLN* 3.7 33.7 - - + +
300B ALA 3.6 3.4 - - - -
301B THR* 3.7 22.2 - - + -
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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