Contacts of the strand formed by residues 279 - 284 (chain A) in PDB entry 5PJP
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 TYR 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A TRP* 3.5 4.4 - - + -
192A HIS* 3.3 28.0 - - - -
193A THR* 3.6 24.8 + - + +
214A VAL* 3.2 6.8 - - - +
215A VAL* 2.9 36.3 + - + -
220A GLY* 3.8 26.7 - - - -
223A LEU* 3.6 31.4 - - + -
224A GLU* 2.6 36.7 + - + +
242A LEU* 3.6 21.1 - - + -
277A TYR* 3.4 20.9 + + - -
278A GLY* 1.3 70.2 - - - +
280A HIS* 1.3 57.9 + - - +
407A EDO 3.3 20.6 - - - -
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Residues in contact with HIS 280 (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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48A LEU* 5.7 0.7 - - + -
189A PHE* 4.0 4.0 - + - -
190A ALA 3.2 5.2 - - - +
191A TRP* 3.3 5.1 - - - -
192A HIS* 2.9 57.6 + + - -
193A THR* 4.6 1.1 - - - -
194A GLU* 2.9 21.3 - - + -
212A TRP* 3.7 27.6 - + + -
213A TYR 3.1 13.7 - - - +
214A VAL* 4.5 7.0 - - + -
274A THR* 3.7 23.3 - - + +
278A GLY 2.9 21.7 + - - +
279A TYR* 1.3 74.5 - - - +
281A ALA* 1.4 60.1 + - - +
402A NI 2.1 33.2 - - + +
404A OGA 3.2 4.8 + - - -
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Residues in contact with ALA 281 (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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126A TRP* 6.2 1.3 - - + -
189A PHE* 3.3 26.6 - - - +
190A ALA 3.9 0.2 - - - -
191A TRP* 3.5 41.3 - - + +
212A TRP* 3.5 3.8 - - - -
213A TYR* 2.8 33.3 + - + +
248A LEU* 4.2 6.7 - - + -
280A HIS* 1.4 74.8 - - - +
282A GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 282 (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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125A TYR* 4.6 1.0 + - - -
126A TRP* 6.1 1.3 - - - -
188A THR* 3.4 6.4 - - - +
189A PHE* 2.9 42.9 + - - +
211A THR 3.0 13.2 - - - -
213A TYR* 4.2 10.5 - - - -
248A LEU* 5.1 1.6 - - - +
281A ALA* 1.3 78.5 - - - +
283A PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 283 (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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121A LEU* 4.9 1.8 - - + -
122A GLU* 4.0 24.2 - - + -
125A TYR* 3.4 62.4 - + + +
126A TRP* 4.3 0.9 - + - -
185A TRP* 4.2 8.7 - + - -
186A LYS 4.8 0.2 - - - +
187A THR 3.1 10.1 - - - +
189A PHE* 3.6 3.0 - - - -
210A LYS* 3.4 3.8 - - - +
211A THR* 2.9 53.0 + - + -
213A TYR* 3.5 29.8 - + - -
282A GLY* 1.3 77.8 - - - +
284A ASN* 1.3 75.3 + - - +
285A HIS* 3.7 21.3 + + - -
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Residues in contact with ASN 284 (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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136A TYR* 3.1 29.9 + - - -
183A GLY* 3.8 4.2 - - - -
184A MET 3.5 14.6 - - - +
185A TRP* 3.6 4.2 - - - -
186A LYS 3.1 24.9 + - - -
187A THR* 2.9 29.3 + - - +
189A PHE* 5.6 1.9 - - - -
209A PRO 3.6 2.2 - - - -
210A LYS* 2.9 29.8 + - - +
283A PHE* 1.3 78.8 - - - +
285A HIS* 1.3 63.9 + - - +
286A GLY 3.4 4.9 - - - +
288A ASN* 3.0 25.5 + - - +
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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