Contacts of the strand formed by residues 308 - 319 (chain C) in PDB entry 5E9W
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 LEU 308 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277C CYS* 5.5 0.7 - - - -
278C PHE* 3.5 20.6 - - + +
279C ASP 4.1 0.2 - - - +
280C ILE 4.0 4.7 - - - +
281C CYS* 3.7 13.2 - - + +
304C ALA 3.6 22.4 + - - +
305C CYS* 3.2 16.3 + - - +
306C GLU 3.3 2.1 - - - +
307C ARG* 1.3 76.9 - - - +
309C SER* 1.3 65.6 + - - +
310C PRO* 3.7 2.4 - - - +
312C GLY 4.4 1.1 - - - -
313C TYR 3.6 39.0 - - - +
314C PHE* 4.1 4.5 - - + +
387C MET* 3.7 30.7 - - + -
474C LYS* 3.3 21.0 - - + -
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Residues in contact with SER 309 (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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194C LYS* 5.8 2.2 - - - -
195C LYS* 5.7 1.6 + - - -
277C CYS* 3.6 24.7 - - - +
278C PHE 2.9 17.1 + - - -
279C ASP* 4.7 9.9 + - - -
307C ARG 3.5 2.0 + - - -
308C LEU* 1.3 76.2 - - - +
310C PRO* 1.3 70.3 - - - +
311C GLY 3.3 0.2 + - - -
312C GLY* 2.8 30.3 + - - -
474C LYS* 3.4 4.9 - - - +
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Residues in contact with PRO 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LYS* 4.0 10.4 - - - -
308C LEU 4.2 2.0 - - - +
309C SER* 1.3 90.0 - - - +
311C GLY* 1.3 59.6 + - - +
312C GLY 3.4 0.2 + - - -
474C LYS* 3.5 13.4 - - + +
475C GLN 3.8 14.8 - - - +
476C GLN* 4.0 29.3 + - + +
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Residues in contact with GLY 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LYS* 3.7 21.8 - - - +
310C PRO* 1.3 71.0 - - - +
312C GLY* 1.3 63.7 + - - +
313C TYR* 3.4 24.6 + - - -
473C GLU* 3.8 15.2 - - - +
474C LYS 2.6 18.8 + - - -
475C GLN 4.9 0.2 - - - -
476C GLN* 5.3 3.7 - - - +
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Residues in contact with GLY 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LYS* 4.3 5.8 - - - +
279C ASP* 3.2 18.4 - - - -
308C LEU* 4.4 7.2 - - - -
309C SER* 2.8 18.8 + - - -
310C PRO 3.2 1.0 + - - -
311C GLY* 1.3 82.2 - - - +
313C TYR* 1.3 59.9 + - - -
387C MET* 4.5 0.2 - - - +
473C GLU* 3.4 3.8 - - - -
474C LYS* 2.8 27.0 + - - +
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Residues in contact with TYR 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C PHE* 3.7 30.5 - + + -
190C LYS* 4.0 30.6 + - + +
191C VAL* 3.9 29.4 - - + -
194C LYS* 5.5 3.0 - - + +
279C ASP 2.9 9.9 + - - +
280C ILE* 3.2 7.9 - - + +
281C CYS 2.7 33.1 + - - +
308C LEU* 3.6 8.2 - - - +
311C GLY 3.4 15.9 + - - -
312C GLY* 1.3 77.0 - - - -
314C PHE* 1.3 54.7 + - - +
315C ILE* 3.9 16.8 - - + -
390C VAL* 4.1 9.4 - - + -
472C PHE 3.3 14.1 - - - +
473C GLU* 3.8 34.2 + - + -
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Residues in contact with PHE 314 (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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281C CYS* 3.4 11.2 - - + -
283C CYS* 3.8 23.8 - - + -
287C CYS* 4.0 13.0 - - - -
300C MET* 6.3 1.3 - - + -
301C LEU* 3.6 27.1 - - + -
304C ALA* 3.6 25.1 - - + -
305C CYS* 3.7 19.7 - - - -
308C LEU* 4.1 5.3 - - + +
313C TYR* 1.3 71.0 - - - +
315C ILE* 1.3 62.4 + - - +
378C LEU* 5.0 2.7 - - + -
382C ALA* 5.6 0.9 - - + -
387C MET* 3.9 16.8 - - + -
470C PHE* 3.7 27.7 - + - -
471C ALA* 3.3 1.9 - - - -
472C PHE* 2.7 59.8 + + + +
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Residues in contact with ILE 315 (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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183C LEU* 4.2 23.1 - - + +
184C ILE* 4.2 26.7 - - + -
187C PHE* 3.9 27.8 - - + -
215C TRP* 5.0 0.9 - - + -
280C ILE* 4.1 17.3 - - + -
281C CYS 2.9 14.0 + - - +
282C SER* 4.0 5.4 - - - +
283C CYS* 2.8 27.2 + - - +
284C GLN* 3.9 9.6 - - - +
313C TYR* 4.0 13.5 - - + +
314C PHE* 1.3 79.3 - - - +
316C GLY* 1.3 59.8 + - - +
470C PHE* 3.4 12.6 - - - +
471C ALA* 3.9 11.9 - - + -
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Residues in contact with GLY 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C LEU* 4.1 3.4 - - - +
283C CYS 3.1 13.2 - - - -
284C GLN* 3.7 9.8 - - - +
315C ILE* 1.3 76.6 - - - +
317C THR* 1.3 68.7 + - - +
469C VAL* 3.4 1.9 - - - +
470C PHE* 2.9 48.6 + - - +
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Residues in contact with THR 317 (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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179C MET* 5.9 2.2 - - + -
180C LYS* 5.2 4.7 - - + -
183C LEU* 4.5 5.4 - - + -
283C CYS 3.3 4.9 + - - +
284C GLN* 2.8 22.8 + - - +
285C PHE* 3.0 59.4 + - + -
286C VAL 4.1 1.9 + - - -
287C CYS* 5.0 1.4 + - - +
316C GLY* 1.3 77.4 - - - +
318C THR* 1.3 63.5 + - - +
395C PHE* 3.7 33.4 - - + -
468C LEU 3.3 7.2 - - - +
469C VAL* 4.0 9.4 - - + -
470C PHE* 3.8 2.6 - - - -
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Residues in contact with THR 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C CYS* 4.1 10.9 - - + +
288C HIS* 3.0 35.2 + - - +
317C THR* 1.3 75.6 - - - +
319C PRO* 1.3 81.2 - - - +
373C VAL* 4.0 21.0 - - + +
375C PHE* 5.3 1.6 - - + -
378C LEU* 5.2 3.1 - - + -
467C TYR* 3.6 7.0 - - - -
468C LEU* 2.8 47.5 + - + +
470C PHE* 4.4 9.9 - - + -
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Residues in contact with PRO 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C HIS* 3.3 22.7 - - + +
318C THR* 1.3 105.5 - - - +
320C ASN* 1.3 62.4 + - - +
321C SER* 3.4 3.5 + - - -
324C LEU* 3.8 14.5 - - + +
358C TYR* 3.4 26.9 - - - +
370C GLU* 3.6 10.8 - - - +
373C VAL* 4.4 10.9 + - + +
466C ILE* 3.6 15.5 - - + +
467C TYR* 3.5 22.4 - - + +
468C LEU* 4.4 0.9 - - - +
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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