Contacts of the strand formed by residues 255 - 260 (chain C) in PDB entry 3QNF
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 GLU 255 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253C ASP 3.6 2.6 + - - -
254C PHE* 1.3 77.1 - - - +
256C SER* 1.3 66.6 + - - +
270C TYR* 3.7 0.5 - - - -
271C ALA 3.1 25.1 + - - +
273C PRO* 4.5 21.1 - - + +
276C ILE* 4.0 17.9 - - + -
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Residues in contact with SER 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C LEU* 5.7 1.2 - - - +
255C GLU* 1.3 79.9 - - - +
257C VAL* 1.3 72.6 + - - +
258C SER* 5.2 2.4 + - - -
268C SER* 5.2 0.9 - - - -
269C VAL 3.4 14.4 - - - -
270C TYR* 3.6 34.8 + - - -
276C ILE* 3.6 7.3 - - - +
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Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715B THR* 5.9 7.0 - - + -
719B GLU* 5.9 3.1 - - - +
256C SER* 1.3 80.9 - - - +
258C SER* 1.3 64.0 + - - +
268C SER* 3.2 3.8 - - - -
269C VAL* 2.9 39.1 + - + +
276C ILE* 4.4 15.3 - - + +
279C ALA* 4.1 21.3 - - + -
280C ASP* 4.7 14.8 - - - +
283C LEU* 4.0 20.0 - - + +
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Residues in contact with SER 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B THR* 5.2 10.0 - - - +
719B GLU* 5.6 1.4 - - - +
256C SER* 5.2 2.8 + - - -
257C VAL* 1.3 73.9 - - - +
259C LYS* 1.3 65.2 + - - +
260C ILE* 5.8 1.1 - - - -
266C LYS* 3.6 24.6 - - - -
267C VAL 3.2 7.2 - - - -
268C SER* 2.6 27.2 + - - -
283C LEU* 3.7 7.3 - - - +
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Residues in contact with LYS 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C SER* 1.3 77.6 - - - +
260C ILE* 1.3 73.0 + - - +
267C VAL* 2.7 35.1 + - - +
283C LEU* 3.9 19.1 - - + -
284C ASP* 3.7 25.1 - - - +
287C VAL* 3.9 28.7 - - + -
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Residues in contact with ILE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C SER* 5.8 0.4 - - - -
259C LYS* 1.3 84.5 - - - +
261C THR* 1.3 78.4 + - - +
264C GLY* 3.7 25.1 - - - +
265C VAL 3.3 1.3 - - - -
266C LYS* 3.5 37.5 - - + +
287C VAL* 4.4 5.3 - - - +
291C GLU* 4.9 0.3 - - - +
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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