Contacts of the strand formed by residues 281 - 288 (chain B) in PDB entry 5C5B
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 ALA 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.6 10.7 - - - +
279B GLN* 6.3 0.2 - - + -
280B LYS* 1.3 85.5 + - - +
282B GLY* 1.3 58.7 + - - +
301B TYR* 3.6 17.7 - - + +
302B PHE 3.2 6.1 - - - -
303B PHE* 3.7 18.8 - - + -
362B GLU* 5.4 1.6 - - - +
366B TRP* 4.1 4.7 - - - -
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Residues in contact with GLY 282 (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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14A GLU* 4.0 5.6 - - - -
281B ALA* 1.3 74.8 - - - +
283B TYR* 1.3 64.3 + - - -
284B LEU* 3.7 1.1 + - - -
301B TYR* 3.8 18.2 - - - -
302B PHE* 2.9 33.5 + - - +
362B GLU* 6.1 0.9 - - - -
366B TRP* 3.9 9.7 - - - -
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Residues in contact with TYR 283 (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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14A GLU* 3.5 16.8 - - - -
15A ASP* 2.2 40.0 + - + -
17A PRO* 3.5 10.2 - - + +
282B GLY* 1.3 71.6 - - - -
284B LEU* 1.3 69.5 + - - +
299B ARG* 3.3 53.8 - - + +
300B LEU* 3.4 18.2 - - - -
301B TYR* 3.8 30.3 - + + -
314B ARG* 3.1 32.7 - - + -
356B GLN 4.6 0.7 - - - +
357B ALA* 5.1 2.4 - - - -
358B GLU* 5.5 1.7 + - - +
366B TRP* 5.2 0.5 + - - -
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Residues in contact with LEU 284 (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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282B GLY 3.7 1.0 + - - +
283B TYR* 1.3 81.3 - - - +
285B ASN* 1.3 66.4 + - - +
286B LEU 3.8 0.9 + - - -
298B GLU 3.6 0.2 - - - +
299B ARG* 3.5 2.7 - - - -
300B LEU 2.9 31.3 + - - +
302B PHE* 3.5 27.9 - - + -
342B PHE* 3.8 21.1 - - + -
355B LEU* 4.0 16.8 - - + -
356B GLN 3.5 17.5 - - - +
357B ALA* 3.8 14.8 - - + -
362B GLU* 5.9 0.2 - - + -
366B TRP* 3.5 51.8 - - + +
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Residues in contact with ASN 285 (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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144A ILE* 6.1 0.2 - - - +
145A ASN* 5.3 2.8 + - - +
148A SER* 2.7 32.7 + - - -
284B LEU* 1.3 72.6 - - - +
286B LEU* 1.3 61.1 + - - +
297B TRP* 3.7 18.9 - - + -
298B GLU 3.5 3.6 - - - +
299B ARG* 3.4 35.9 + - - +
338B ARG* 4.4 1.5 - - - +
355B LEU* 3.3 9.1 - - - -
356B GLN* 3.0 59.4 + - + +
357B ALA 5.9 0.8 + - - -
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Residues in contact with LEU 286 (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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284B LEU 3.8 1.2 + - - -
285B ASN* 1.3 71.4 - - - +
287B ARG* 1.3 78.2 + - - +
288B ASN* 3.7 4.7 + - + +
297B TRP* 3.4 3.7 - - - -
298B GLU* 2.9 39.3 + - + +
300B LEU* 3.9 22.2 - - + -
302B PHE* 3.9 19.7 - - + -
311B CYS* 4.9 1.6 - - - -
322B ILE* 4.5 19.3 - - + -
353B ILE* 4.4 22.4 - - + -
354B ILE 3.6 6.7 - - - +
355B LEU* 3.6 18.8 - - + -
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Residues in contact with ARG 287 (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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286B LEU* 1.3 85.5 - - - +
288B ASN* 1.3 60.9 + - - +
289B LYS* 3.6 42.8 + - - +
295B THR* 3.3 21.6 + - - +
296B THR 3.4 4.5 - - - +
297B TRP* 3.5 43.1 - - + -
335B CYS* 3.6 15.5 - - - -
336B GLU* 3.3 17.2 + - - +
353B ILE* 6.0 0.3 - - - +
354B ILE* 3.1 45.5 + - + +
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Residues in contact with ASN 288 (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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286B LEU* 3.7 6.0 + - + +
287B ARG* 1.3 73.6 + - - +
289B LYS* 1.3 61.0 + - - +
290B THR* 3.3 28.3 + - - +
294B THR 4.5 0.2 - - - +
295B THR* 3.6 2.9 - - - -
296B THR* 2.8 51.2 + - - +
298B GLU* 6.4 1.3 - - + -
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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