Contacts of the strand formed by residues 280 - 284 (chain B) in PDB entry 4GGD
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 ILE 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B SER 4.0 0.2 - - - +
276B TRP* 3.6 3.8 - - - -
277B ASN* 2.9 43.7 + - + +
279B TYR* 1.3 100.6 - - + +
281B LEU* 1.3 61.9 + - - +
282B SER* 3.9 12.9 + - - +
292B HIS* 3.9 25.8 - - + +
293B HIS 3.5 13.5 - - - +
294B ASP* 3.6 22.0 - - + +
302B VAL* 4.6 10.5 - - + -
317B TRP* 4.8 8.7 - - + -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ALA* 3.4 25.8 - - + -
250B VAL* 3.7 22.7 - - + -
252B LEU* 5.4 0.9 - - + -
264B MET* 4.5 10.3 - - + -
274B LEU* 4.3 11.2 - - + -
275B SER 3.8 17.5 - - - +
276B TRP* 3.8 34.8 - - + +
279B TYR 3.6 1.2 + - - -
280B ILE* 1.3 72.9 - - - +
282B SER* 1.3 71.9 + - - +
293B HIS* 2.8 48.3 + - + +
295B VAL* 3.8 16.8 - - + -
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 3.3 4.5 - - - -
275B SER 2.8 42.6 + - - -
280B ILE* 4.0 1.7 - - - +
281B LEU* 1.3 77.6 - - - +
283B SER* 1.3 61.1 + - - +
290B ILE* 4.7 1.3 - - - -
291B HIS 3.3 5.4 - - - -
292B HIS* 2.8 30.4 + - - -
315B LEU* 3.6 14.2 - - - +
317B TRP* 3.0 22.5 + - - -
324B LEU* 4.3 6.3 - - - -
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Residues in contact with SER 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL* 4.1 4.3 - - - -
267B HIS* 2.7 29.5 + - - -
271B VAL* 3.8 10.3 - - - -
273B SER 3.4 4.3 - - - -
274B LEU* 3.8 16.2 - - - -
281B LEU 3.9 0.2 + - - -
282B SER* 1.3 76.7 - - - +
284B GLY* 1.3 59.8 + - - +
290B ILE* 3.2 5.5 - - - +
291B HIS 2.9 28.5 + - - -
293B HIS* 2.9 25.7 + - - -
315B LEU* 3.6 4.0 - - - -
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Residues in contact with GLY 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B HIS* 4.5 0.4 - - - -
271B VAL* 3.3 9.3 - - - +
272B GLY 3.3 21.0 + - - -
273B SER* 2.8 28.0 + - - -
283B SER* 1.3 74.6 - - - +
285B SER* 1.3 61.7 + - - -
289B HIS 3.7 6.1 - - - -
290B ILE* 4.3 1.6 - - - -
312B VAL* 4.0 12.6 - - - -
315B LEU* 3.5 7.2 - - - +
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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
------------------------------------------------------------
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