Contacts of the strand formed by residues 316 - 324 (chain D) in PDB entry 5FLZ
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 PHE 316 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299D LEU* 5.1 11.7 - - + -
308D THR* 4.0 10.8 - - - -
312D ASN* 3.2 41.5 - - + -
315D TYR* 1.3 86.9 - - - +
317D ASN* 1.3 62.9 + - - +
318D VAL 4.6 7.4 - - - +
319D TYR* 4.2 27.4 - + + -
344D PHE 5.3 0.2 - - - -
345D PRO* 3.6 25.4 - - + -
346D SER* 3.3 35.7 + - - +
347D TRP* 3.4 18.7 - - + -
354D VAL* 4.6 0.7 - - - +
376D MET* 5.4 2.0 - - + -
378D SER* 4.5 16.4 - - - -
379D ASN 3.9 5.6 - - - +
380D MET* 3.8 13.2 - - + -
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Residues in contact with ASN 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D PRO* 4.3 20.1 - - + +
265D LEU* 3.9 23.8 - - - +
315D TYR* 3.5 33.7 + - + -
316D PHE* 1.3 72.6 - - - +
318D VAL* 1.4 63.2 + - - +
354D VAL* 3.3 22.9 - - - +
379D ASN* 2.9 45.0 + - - +
380D MET* 3.4 1.2 - - - +
381D SER* 3.4 19.9 - - - +
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Residues in contact with VAL 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D LEU* 3.4 52.0 - - + +
261D PRO* 4.8 1.3 - - + -
268D LEU* 5.3 4.5 - - + -
316D PHE* 3.6 4.7 - - - +
317D ASN* 1.4 79.7 + - + +
319D TYR* 1.3 81.1 + - - +
320D ASN* 5.4 2.7 - - + +
354D VAL* 3.6 25.4 - - + +
356D ILE* 5.2 1.1 - - + +
377D LEU 5.2 0.2 - - - -
378D SER* 3.5 4.4 - - - -
379D ASN* 3.0 52.0 + - + +
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Residues in contact with TYR 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D LEU* 2.8 30.3 + - - +
297D ASP* 4.3 6.7 + - - -
299D LEU* 4.7 9.7 - - + +
316D PHE* 4.2 24.7 - + + -
318D VAL* 1.3 85.2 - - - +
320D ASN* 1.4 79.7 + - - +
321D THR* 3.5 22.2 - - + -
344D PHE* 6.3 1.8 - - + -
345D PRO* 4.2 19.7 - - + -
347D TRP* 6.3 0.2 - - + -
354D VAL 3.6 3.5 + - - +
355D ASN* 3.5 19.7 - - + -
356D ILE* 2.9 28.3 + - - +
376D MET* 3.6 28.2 - - + +
377D LEU 3.9 0.9 - - - -
378D SER* 3.1 16.8 - - - +
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Residues in contact with ASN 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D VAL* 6.0 0.6 - - - +
255D ILE* 6.2 0.2 - - + -
259D LEU* 3.8 27.9 - - + +
268D LEU* 5.2 3.8 - - - +
318D VAL* 5.5 2.9 - - - +
319D TYR* 1.4 80.3 - - - +
321D THR* 1.4 62.7 + - - +
322D ILE* 4.0 20.0 - - - +
356D ILE* 3.3 18.6 - - + -
358D ARG* 5.6 2.5 - - - +
376D MET* 3.5 1.6 - - - -
377D LEU* 2.9 77.4 + - - +
378D SER* 5.0 0.7 - - - -
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Residues in contact with THR 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D LEU* 4.0 36.6 - - + -
319D TYR* 3.5 22.4 - - + -
320D ASN* 1.4 74.9 - - - +
322D ILE* 1.4 58.5 + - - +
323D ILE* 4.2 15.5 - - + -
356D ILE 2.7 16.8 + - - -
357D GLY* 3.2 7.4 - - - -
358D ARG* 2.8 34.0 + - - +
375D MET 3.8 2.9 - - - +
376D MET* 5.8 0.7 - - - -
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Residues in contact with ILE 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D SER* 4.3 11.0 - - - +
238D VAL* 3.9 25.1 - - + +
240D ASN* 5.5 2.5 - - + -
292D TYR* 4.0 0.3 + - - -
320D ASN* 4.0 20.0 - - - +
321D THR* 1.4 71.5 - - - +
323D ILE* 1.4 70.0 + - - +
324D GLY* 4.9 1.1 - - - +
358D ARG* 3.7 44.6 - - - +
360D SER* 6.5 0.2 - - - -
374D GLY* 3.0 8.6 - - - -
375D MET* 2.9 62.8 + - + +
377D LEU* 5.2 0.2 - - + -
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Residues in contact with ILE 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D HIS* 6.1 2.5 - - - +
292D TYR* 3.4 36.8 - - + +
296D LEU* 5.1 2.7 - - + -
321D THR* 4.2 17.0 - - + -
322D ILE* 1.4 82.3 - - - +
324D GLY* 1.4 58.4 + - - +
325D ASN 4.1 16.2 - - - +
332D SER* 4.7 8.5 - - - +
335D MET* 5.7 4.0 - - + -
357D GLY* 5.7 2.2 - - - -
358D ARG* 2.8 23.4 + - - +
359D ARG* 3.7 30.9 - - + -
360D SER* 3.0 31.5 + - - +
372D VAL* 4.3 2.9 - - + -
373D SER 4.2 0.9 - - - +
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Residues in contact with GLY 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D ASN* 6.0 3.1 - - - -
322D ILE* 4.0 3.3 + - - +
323D ILE* 1.4 69.9 - - - +
325D ASN* 1.4 68.3 + - - +
360D SER* 3.4 6.1 - - - -
361D PRO 5.3 1.3 - - - -
362D TYR* 3.6 15.5 - - - -
372D VAL* 3.3 3.4 - - - +
373D SER* 3.0 34.5 + - - +
374D GLY* 4.6 0.4 - - - -
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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