Contacts of the strand formed by residues 324 - 329 (chain A) in PDB entry 5FN2
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 ASN 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A MET* 3.6 8.7 - - - +
260A LEU* 3.4 3.3 - - - +
261A LYS* 3.0 56.3 + - + +
263A ILE* 3.2 32.3 - - - +
273A ASP* 5.9 1.6 - - - +
274A ARG 3.4 5.7 + - - -
275A VAL* 2.9 23.1 - - + +
276A VAL* 2.6 31.2 + - - -
322A PRO 4.1 1.0 + - - +
323A ARG* 1.3 74.3 - - - +
325A VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 325 (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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259A MET* 3.1 11.2 - - - +
260A LEU* 2.8 58.0 + - + -
276A VAL* 3.2 23.1 - - + +
278A ALA* 4.8 0.4 - - + -
312A LEU* 4.2 9.9 - - + -
324A ASN* 1.3 83.6 + - - +
326A MET* 1.3 64.8 - - - +
327A PHE* 3.9 21.5 - - + -
498A LEU* 3.9 27.4 - - + +
502A ALA* 4.3 16.4 - - + -
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Residues in contact with MET 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TRP* 4.2 15.3 - - - +
258A SER 3.6 16.6 - - - +
259A MET* 3.7 14.4 - - + -
275A VAL* 5.1 7.6 - - + -
276A VAL 2.8 17.2 + - - +
277A VAL* 3.8 23.1 - - + -
278A ALA* 2.8 29.5 + - - +
325A VAL* 1.3 73.2 - - - +
327A PHE* 1.3 60.8 + - - +
328A VAL* 3.4 32.7 + - + -
330A PHE* 4.9 1.3 - - + -
343A MET* 3.5 29.8 - - + -
347A MET* 5.5 4.3 - - - -
352A PHE* 5.1 2.0 - - + -
354A VAL* 5.6 9.2 - - + -
430A PHE* 5.7 1.6 - - + -
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Residues in contact with PHE 327 (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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257A TRP 3.6 1.0 - - - -
258A SER* 2.8 44.9 + - - -
259A MET 5.0 8.7 - - - -
260A LEU* 5.2 2.7 - - + -
278A ALA* 3.6 13.2 - - + -
305A GLN* 3.7 18.8 - - + +
308A ALA* 4.1 1.8 - - + -
309A ALA* 3.2 49.8 - - + -
312A LEU* 3.5 26.5 - - + -
313A GLN* 5.3 2.9 - - - -
325A VAL* 3.9 17.7 - - + -
326A MET* 1.3 69.1 - - - +
328A VAL* 1.3 59.5 - - - +
329A PHE* 3.8 12.6 - - + -
498A LEU* 3.4 33.2 - - + -
571A LEU* 5.0 0.9 - - + -
575A THR* 5.5 2.7 - - + -
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Residues in contact with VAL 328 (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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255A ASN* 4.8 3.4 - - + -
256A VAL 3.5 12.1 - - - +
257A TRP* 4.4 3.6 - - + +
277A VAL* 4.0 8.7 - - + -
278A ALA 2.8 20.1 + - - +
279A ALA* 4.0 3.6 - - - -
280A THR* 3.2 14.8 + - - -
305A GLN* 2.8 17.2 + - - -
326A MET* 3.4 33.7 - - + +
327A PHE* 1.3 72.1 - - - +
329A PHE* 1.3 68.7 + - - +
330A PHE* 3.3 50.3 - - + -
343A MET* 4.6 3.8 - - + -
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Residues in contact with PHE 329 (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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255A ASN* 3.4 3.5 - - - +
256A VAL* 2.8 47.5 + - + +
280A THR* 3.7 10.3 - - - -
282A LEU* 3.5 40.2 - - + +
302A PHE* 3.6 25.4 - + + -
305A GLN* 3.5 19.7 - - + -
306A LEU* 3.3 36.3 - - + -
327A PHE* 3.8 15.5 - + + -
328A VAL* 1.3 80.1 - - - +
330A PHE* 1.3 63.5 + - - +
331A GLN 3.8 0.5 + - - -
567A VAL* 4.4 3.1 - - + -
571A LEU* 3.4 25.4 - - + -
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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