Contacts of the strand formed by residues 286 - 291 (chain A) in PDB entry 4K81
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 SER 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A SER* 4.2 4.0 + - - -
282A GLU* 3.5 24.0 + - - +
283A PHE* 3.4 8.4 - - - +
284A GLY 3.6 0.2 - - - -
285A ASN* 1.3 81.6 + - - +
287A ASP* 1.3 64.0 + - - +
288A ILE* 4.5 1.3 - - - +
308A PHE* 4.2 14.8 - - - +
309A LYS 3.3 11.4 - - - -
310A PRO* 3.5 22.7 - - - +
311A ASN* 3.9 1.6 - - - -
320A LYS* 4.9 3.6 + - - -
341A LYS* 3.0 26.0 + - - +
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Residues in contact with ASP 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLU* 4.9 0.2 - - - +
162A ARG* 3.5 33.3 + - - +
168A GLU* 4.6 1.4 - - - +
176A ASN* 5.5 6.1 + - - +
286A SER* 1.3 74.1 - - - +
288A ILE* 1.3 64.9 + - - +
289A TYR* 3.4 29.3 + - + +
308A PHE* 3.3 6.2 - - - -
309A LYS 3.0 31.9 + - - +
311A ASN* 4.1 12.1 + - - +
341A LYS* 3.6 9.5 + - - +
342A TYR* 3.6 13.7 + - - -
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ARG* 3.1 25.5 - - - +
283A PHE* 3.5 22.0 - - + -
286A SER 4.5 3.4 - - - +
287A ASP* 1.3 81.7 + - - +
289A TYR* 1.3 66.7 + - - +
290A VAL* 5.8 0.3 - - - +
306A PHE* 4.7 2.5 - - + -
307A CYS 3.6 3.4 - - - +
308A PHE* 3.8 20.0 - - + -
334A VAL* 4.2 27.5 - - + +
337A ILE* 3.2 40.8 - - + -
338A ARG* 4.7 14.4 - - + +
341A LYS* 4.5 14.3 - - + +
342A TYR* 5.7 2.2 + - + +
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Residues in contact with TYR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLU* 2.6 39.1 + - - -
155A LEU* 3.7 23.0 - - + +
160A VAL* 3.5 31.4 - - + -
161A GLU* 3.5 21.3 - - - -
162A ARG* 3.8 13.9 - - + -
287A ASP* 3.4 37.3 + - + +
288A ILE* 1.3 76.5 - - - +
290A VAL* 1.3 65.1 + - - +
306A PHE* 3.1 9.0 - - - +
307A CYS* 3.0 41.5 + - - -
309A LYS* 3.9 23.1 + - + +
319A LEU* 6.0 0.2 - - + -
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 3.2 2.8 - - - -
161A GLU* 2.8 40.6 + - + +
162A ARG* 5.1 1.1 - - - +
288A ILE 5.8 0.2 - - - +
289A TYR* 1.3 76.0 - - - +
291A SER* 1.3 70.1 + - - +
305A GLY 3.9 2.9 - - - -
306A PHE* 4.6 0.2 - - + -
330A ARG* 3.3 38.1 - - + +
334A VAL* 3.9 35.4 - - + -
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Residues in contact with SER 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLY 3.3 11.7 - - - -
160A VAL* 4.0 10.8 - - - +
161A GLU* 5.7 0.4 - - - -
289A TYR 4.4 0.2 + - - -
290A VAL* 1.3 83.7 - - - +
292A LEU* 1.3 68.2 + - - +
294A GLY 6.1 0.4 - - - -
303A ASN 3.6 6.4 + - - -
305A GLY* 3.1 37.5 + - - -
306A PHE* 5.7 0.2 - - - -
330A ARG* 3.6 9.7 + - - -
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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