Contacts of the strand formed by residues 403 - 414 (chain D) in PDB entry 3GV5
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 403 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308D PHE* 3.9 6.3 - - + -
310D LYS* 3.5 1.4 - - - -
311D CYS* 3.0 48.8 + - + +
346D ILE* 4.5 15.7 - - + -
347D ARG 3.3 12.3 - - - +
348D ARG* 4.3 17.3 - - + +
391D PHE* 3.5 36.8 - - + -
395D VAL* 4.8 4.5 - - + -
401D PHE* 3.9 22.9 - - + -
402D HIS* 1.3 87.8 - - - +
404D THR* 1.3 63.0 + - - +
405D LEU 4.3 9.2 - - - +
406D LEU* 4.6 9.6 - - + -
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Residues in contact with THR 404 (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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307D SER* 3.5 0.3 - - - -
308D PHE* 3.1 34.5 + - - +
309D LYS* 3.3 25.6 - - - +
347D ARG* 2.9 50.1 + - - +
348D ARG 4.3 3.3 + - - -
349D TYR* 3.9 26.6 - - + +
402D HIS* 4.2 0.6 + - - +
403D LEU* 1.3 73.8 - - - +
405D LEU* 1.3 56.8 + - - +
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Residues in contact with LEU 405 (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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305D GLU* 3.6 11.4 - - - +
306D ASP 3.5 16.4 - - - +
307D SER* 4.3 7.4 - - - -
308D PHE* 3.7 6.0 - - - -
345D ILE* 4.3 10.3 - - + +
346D ILE* 3.5 5.6 - - - +
347D ARG* 3.2 58.5 + - + +
357D ARG* 3.4 37.2 - - - +
403D LEU* 4.3 3.3 - - - +
404D THR* 1.3 79.2 + - - +
406D LEU* 1.3 84.5 - - - +
407D SER* 4.0 14.4 - - - +
840F T 4.9 2.0 - - - +
841F C 5.5 0.2 - - - +
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Residues in contact with LEU 406 (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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305D GLU* 3.4 2.6 - - - +
306D ASP* 3.0 31.7 + - - +
308D PHE* 3.6 21.2 - - + -
311D CYS* 4.6 7.9 - - - -
317D ALA* 4.0 30.3 - - - +
320D LYS* 4.3 11.0 - - + -
321D ILE* 4.3 11.7 - - + -
324D LEU* 3.5 15.2 - - + +
344D LEU* 4.1 16.2 - - + -
345D ILE 3.4 4.9 - - - +
346D ILE* 3.8 27.1 - - + -
391D PHE* 4.4 8.3 - - + -
403D LEU* 4.6 7.4 - - + -
405D LEU* 1.3 79.8 - - - +
407D SER* 1.3 59.0 + - - +
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Residues in contact with SER 407 (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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303D SER* 5.3 3.8 - - - -
304D GLU 3.2 8.7 - - - -
305D GLU* 3.2 37.2 + - - -
324D LEU* 3.9 1.3 - - - -
344D LEU* 3.5 6.3 - - - +
345D ILE* 2.8 68.4 + - - +
357D ARG* 4.1 1.4 + - - -
405D LEU* 4.0 1.8 - - - +
406D LEU* 1.3 71.9 - - - +
408D VAL* 1.3 66.1 + - - +
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Residues in contact with VAL 408 (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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303D SER* 3.2 4.1 - - - -
304D GLU 3.0 29.9 + - - -
321D ILE* 4.1 23.3 - - + +
324D LEU* 4.1 26.7 - - + -
325D LEU* 4.6 8.1 - - + +
328D LEU* 3.4 23.5 - - + +
342D VAL* 4.0 18.4 - - + -
343D ARG 3.5 9.2 - - - +
344D LEU* 4.2 10.5 - - + -
387D LEU* 4.1 13.0 - - + -
407D SER* 1.3 78.4 - - - +
409D CYS* 1.3 64.1 + - - +
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Residues in contact with CYS 409 (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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301D SER* 4.0 17.0 - - - -
302D PHE 3.4 7.9 - - - -
303D SER* 3.8 13.2 - - - -
328D LEU* 4.4 0.9 - - - -
342D VAL* 3.5 6.6 - - - +
343D ARG* 2.8 47.5 + - + +
345D ILE* 4.0 17.5 - - + -
407D SER 4.3 0.2 - - - -
408D VAL* 1.3 77.0 - - - +
410D PHE* 1.3 76.0 + - - +
411D CYS* 4.2 10.9 + - - -
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Residues in contact with PHE 410 (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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301D SER* 3.3 5.0 - - - -
302D PHE* 2.7 46.6 + - + +
325D LEU* 3.7 21.5 - - + -
328D LEU* 3.8 29.3 - - + +
329D LEU* 3.6 26.7 - - + -
332D VAL* 3.6 23.3 - - + -
339D PRO* 3.7 21.1 - - + -
341D THR 3.7 7.0 - - - -
342D VAL* 3.7 29.2 - - + -
364D ILE* 3.8 11.9 - - + -
371D LYS* 4.3 6.5 - - - -
383D MSE 3.7 11.7 - - + -
409D CYS* 1.3 72.1 - - - +
411D CYS* 1.3 60.8 + - - +
413D LEU* 4.3 3.5 - - - +
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Residues in contact with CYS 411 (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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300D GLN 3.8 15.3 - - - +
301D SER* 3.9 10.1 - - - -
339D PRO* 3.8 2.1 - - - +
340D HIS 3.3 3.8 + - - -
341D THR* 3.1 40.7 + - - +
343D ARG* 4.0 26.7 - - - -
361D GLN* 5.7 0.9 - - - -
409D CYS* 4.3 9.2 - - - -
410D PHE* 1.3 77.6 - - - +
412D ASN* 1.3 77.3 + - - +
413D LEU* 3.4 4.9 - - - -
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Residues in contact with ASN 412 (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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300D GLN 4.0 4.0 + - - -
340D HIS* 2.9 38.1 + - - +
341D THR* 3.1 25.8 - - + +
411D CYS* 1.3 79.2 - - - +
413D LEU* 1.3 60.8 + - - +
414D LYS* 3.3 26.2 + - - +
865E G 5.8 4.2 + - - -
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Residues in contact with LEU 413 (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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299D PRO 3.3 25.8 - - - +
300D GLN* 3.5 23.4 + - - +
301D SER* 3.8 2.5 - - - +
302D PHE* 3.6 39.3 - - + -
337D ARG* 3.6 29.8 + - + +
338D LYS* 3.4 4.9 - - - +
339D PRO* 3.6 33.7 - - + -
410D PHE 4.3 0.2 - - - +
411D CYS* 4.2 9.4 - - - -
412D ASN* 1.3 73.4 + - - +
414D LYS* 1.3 66.4 + - - +
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Residues in contact with LYS 414 (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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337D ARG* 3.5 6.9 - - - +
338D LYS* 2.9 32.7 + - - +
340D HIS* 3.4 39.4 - - + +
412D ASN* 3.3 33.9 + - - +
413D LEU* 1.3 80.7 - - - +
415D ALA* 1.3 66.8 + - - +
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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