Contacts of the strand formed by residues 308 - 319 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277D CYS* 5.7 0.4 - - - -
278D PHE* 3.3 18.8 - - + +
279D ASP 4.0 2.2 - - - -
280D ILE 4.0 3.8 - - - -
281D CYS* 3.7 14.4 - - + +
304D ALA 3.5 23.7 + - - +
305D CYS* 3.2 16.7 + - - +
306D GLU 4.3 0.9 - - - +
307D ARG* 1.3 77.4 - - - +
309D SER* 1.3 67.2 + - - +
310D PRO* 3.8 1.4 - - - +
312D GLY 4.3 1.1 - - - -
313D TYR 3.6 38.1 - - - +
314D PHE* 3.9 4.3 - - + -
387D MET* 3.6 30.7 - - + -
474D LYS* 3.2 23.7 - - + +
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Residues in contact with SER 309 (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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195D LYS* 4.5 6.1 - - - -
277D CYS* 3.7 20.1 - - - +
278D PHE 2.8 20.1 + - - -
279D ASP* 4.2 12.3 + - - -
307D ARG 3.3 2.2 + - - -
308D LEU* 1.3 76.4 - - - +
310D PRO* 1.3 75.2 - - - +
311D GLY 3.3 0.2 + - - -
312D GLY* 2.8 22.5 + - - -
474D LYS* 3.5 4.3 - - - +
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Residues in contact with PRO 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LYS* 4.0 9.2 + - - -
308D LEU 3.8 2.2 - - - +
309D SER* 1.3 88.1 - - - +
311D GLY* 1.3 58.7 + - - +
312D GLY 3.5 0.2 + - - -
474D LYS* 3.9 12.6 - - + +
475D GLN 4.2 11.2 - - - +
476D GLN* 4.2 22.9 - - + -
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Residues in contact with GLY 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D VAL* 5.1 0.3 - - - +
194D LYS* 2.9 37.8 + - - -
195D LYS* 4.3 5.7 + - - -
310D PRO* 1.3 72.5 - - - +
312D GLY* 1.3 64.1 + - - +
313D TYR* 3.4 11.4 - - - -
473D GLU* 3.7 7.4 - - - +
474D LYS 2.9 19.1 + - - -
475D GLN 5.1 0.2 - - - -
476D GLN* 6.0 0.2 - - - +
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Residues in contact with GLY 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LYS* 4.1 7.3 - - - +
279D ASP* 3.2 18.4 - - - -
308D LEU* 4.3 7.4 - - - -
309D SER 2.8 17.5 + - - -
310D PRO 3.2 1.2 + - - -
311D GLY* 1.3 81.6 - - - +
313D TYR* 1.3 60.9 + - - -
387D MET* 4.5 0.2 - - - +
473D GLU* 3.4 3.5 - - - -
474D LYS* 2.8 26.8 + - - -
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Residues in contact with TYR 313 (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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367B ASP* 5.0 9.5 + - - +
187D PHE* 3.6 30.1 - + + -
190D LYS* 3.8 29.7 - - + +
191D VAL* 3.6 28.5 - - + -
194D LYS* 2.9 28.2 + - - -
279D ASP 3.0 7.8 + - - +
280D ILE* 3.3 8.6 - - + +
281D CYS 2.8 31.9 + - - +
308D LEU* 3.6 6.7 - - - +
311D GLY 3.4 10.5 - - - -
312D GLY* 1.3 76.5 - - - -
314D PHE* 1.3 55.3 + - - +
315D ILE* 3.9 16.6 - - + -
390D VAL* 4.2 8.5 - - + -
472D PHE 3.2 13.9 - - - +
473D GLU* 3.7 25.1 + - + -
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Residues in contact with PHE 314 (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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281D CYS* 3.5 11.9 - - + -
283D CYS* 3.9 23.6 - - + -
287D CYS* 3.9 12.6 - - - -
300D MET* 6.4 1.1 - - + -
301D LEU* 3.6 28.9 - - + -
304D ALA* 3.7 24.0 - - + -
305D CYS* 3.6 15.9 - - - -
308D LEU* 3.9 9.7 - - + +
313D TYR* 1.3 70.3 - - - +
315D ILE* 1.3 61.6 + - - +
378D LEU* 5.1 2.7 - - + -
382D ALA* 5.6 0.2 - - + -
387D MET* 3.9 17.0 - - + -
470D PHE* 3.6 27.9 - + - -
471D ALA* 3.3 2.1 - - - -
472D PHE* 2.7 61.5 + + + +
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Residues in contact with ILE 315 (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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183D LEU* 4.3 17.5 - - + +
184D ILE* 4.3 26.9 - - + -
187D PHE* 3.8 30.7 - - + -
215D TRP* 5.1 0.9 - - + -
280D ILE* 4.1 17.5 - - + -
281D CYS 3.0 14.7 + - - +
282D SER* 3.9 15.0 - - - +
283D CYS* 2.8 28.8 + - - +
284D GLN* 4.0 4.9 - - - +
313D TYR* 4.0 12.8 - - + -
314D PHE* 1.3 78.0 - - - +
316D GLY* 1.3 58.9 + - - +
470D PHE* 3.3 11.7 - - - +
471D ALA* 3.8 13.0 - - + -
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Residues in contact with GLY 316 (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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183D LEU* 4.1 2.8 - - - +
283D CYS 3.0 13.2 - - - -
284D GLN* 3.8 8.7 - - - +
315D ILE* 1.3 76.8 - - - +
317D THR* 1.3 65.2 + - - +
469D VAL* 3.4 5.7 - - - +
470D PHE* 2.9 48.3 + - - +
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Residues in contact with THR 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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179D MET* 6.0 2.5 - - + -
180D LYS* 5.3 3.6 - - + +
183D LEU* 4.6 4.9 - - + -
283D CYS 3.3 4.7 + - - +
284D GLN* 2.8 22.8 + - - +
285D PHE* 3.0 58.6 + - + -
286D VAL 4.1 2.3 + - - -
287D CYS* 5.0 1.4 + - - +
316D GLY* 1.3 76.8 - - - +
318D THR* 1.3 65.0 + - - +
395D PHE* 3.6 29.2 - - + -
467D TYR* 4.0 2.2 - - - -
468D LEU 3.3 5.6 - - - +
469D VAL* 4.0 9.2 - - + -
470D PHE* 3.7 2.4 - - - -
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Residues in contact with THR 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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287D CYS* 4.1 6.6 - - + +
288D HIS* 2.8 34.9 + - - +
317D THR* 1.3 77.1 - - - +
319D PRO* 1.3 81.3 - - - +
373D VAL* 4.0 20.7 - - + +
375D PHE* 5.4 1.3 - - + -
378D LEU* 5.3 2.9 - - + -
467D TYR* 3.3 7.1 - - - -
468D LEU* 2.9 42.5 + - + +
470D PHE* 4.1 14.6 - - + -
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Residues in contact with PRO 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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288D HIS* 3.3 16.8 - - + +
318D THR* 1.3 104.9 - - - +
320D ASN* 1.3 61.9 + - - +
321D SER* 3.5 3.9 + - - -
324D LEU* 3.8 13.9 - - + +
358D TYR* 3.5 26.5 - - - +
360D PHE* 6.6 0.2 - - + -
370D GLU* 3.7 10.1 - - - +
373D VAL* 4.5 10.0 + - - +
466D ILE* 3.7 15.7 - - + +
467D TYR* 3.4 28.0 - - + +
468D LEU* 4.3 1.2 - - - +
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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