Contacts of the strand formed by residues 358 - 364 (chain D) in PDB entry 1DVM
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 358 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189D PHE* 4.4 3.6 - + - -
237D ILE* 4.0 12.6 - - + -
238D ALA 3.6 12.3 - - - +
239D ALA* 4.1 13.9 - - + -
240D PRO* 4.6 0.2 - - - -
247D LEU* 3.8 9.8 - - - +
275D LEU* 4.0 14.8 - - + -
276D PRO* 3.8 14.6 - - + -
278D PHE* 3.6 28.3 - + - -
354D ILE* 3.3 22.7 - - + -
356D ARG 3.7 8.5 - - - +
357D PRO* 1.3 76.4 - - - +
359D LEU* 1.3 71.5 + - - +
360D PHE* 4.5 8.1 - - + -
375D GLN* 3.4 3.6 - - - +
376D VAL* 2.9 70.8 + - + +
377D MET* 5.4 0.4 - - - +
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Residues in contact with LEU 359 (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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20D PHE* 4.5 0.7 - - + -
237D ILE* 3.5 3.3 - - - -
238D ALA* 2.8 43.8 + - + +
247D LEU* 3.8 13.4 - - + +
250D LEU* 4.0 21.8 - - + -
251D THR* 3.6 23.6 - - + -
254D LEU* 3.4 28.3 - - + -
262D TRP* 5.3 0.2 - - + -
358D PHE* 1.3 77.5 - - - +
360D PHE* 1.3 75.8 + - - +
361D VAL* 4.6 2.9 - - + -
373D MET* 4.0 19.1 - - + -
374D GLY 2.9 27.1 - - - +
375D GLN* 4.5 4.3 - - + +
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Residues in contact with PHE 360 (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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33D VAL* 4.0 13.9 - - + -
235D MET* 3.8 32.1 - - + -
236D PHE 3.2 11.7 - - - +
237D ILE* 4.8 1.3 - - + -
278D PHE* 3.9 10.8 - + - -
326D ILE* 3.9 33.4 - - + -
358D PHE* 4.5 8.3 - - + -
359D LEU* 1.3 76.3 - - - +
361D VAL* 1.3 69.9 + - - +
362D VAL* 4.4 4.3 - - + -
372D PHE 4.5 1.3 - - - -
373D MET* 3.0 41.8 - - - +
374D GLY* 3.0 36.5 + - - -
375D GLN 4.3 0.7 - - - -
376D VAL* 3.6 30.7 - - + -
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Residues in contact with VAL 361 (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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234D SER 3.5 0.9 - - - +
235D MET* 3.2 4.2 - - - +
236D PHE* 2.6 49.6 + - + +
238D ALA* 6.4 0.2 - - + -
254D LEU* 4.5 19.3 - - + -
259D ILE* 4.3 18.8 - - + -
262D TRP* 4.7 9.4 - - + -
359D LEU* 4.6 4.5 - - + -
360D PHE* 1.3 81.7 - - - +
362D VAL* 1.3 68.7 - - - +
363D ARG* 4.1 3.4 - - + +
370D VAL* 4.2 23.6 - - + -
372D PHE 3.4 8.7 - - - +
373D MET* 4.1 18.6 - - + +
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Residues in contact with VAL 362 (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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171D PHE* 3.8 35.9 - - + -
228D TYR* 4.3 6.7 - - + -
233D LEU* 4.6 9.6 - - + -
234D SER 3.4 6.7 - - - +
235D MET* 3.7 32.3 - - + -
360D PHE* 4.4 4.5 - - + -
361D VAL* 1.3 77.0 - - - +
363D ARG* 1.3 66.0 + - - +
370D VAL* 3.5 4.0 - - - -
371D LEU* 2.8 30.5 + - + -
372D PHE* 2.8 36.2 + - + +
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Residues in contact with ARG 363 (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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233D LEU* 3.2 10.9 - - - +
234D SER* 2.9 35.9 + - - +
236D PHE* 3.4 29.2 - - + -
256D ALA 5.4 2.2 + - - -
259D ILE* 4.1 15.2 - - + +
260D SER* 4.3 13.1 + - - -
263D LYS* 3.0 29.0 - - - +
361D VAL* 5.0 4.7 - - + -
362D VAL* 1.3 76.3 - - - +
364D HIS* 1.3 59.1 + - - +
365D ASN* 2.8 51.2 + - - +
368D GLY* 3.3 29.6 + - - +
369D THR 3.1 13.5 - - - +
370D VAL* 4.4 3.8 - - + -
371D LEU* 4.5 1.1 - - - +
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Residues in contact with HIS 364 (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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78D LEU* 4.3 4.1 - - + +
81D GLU* 3.2 39.3 + - + +
82D LEU* 3.8 21.6 - - + +
86D TRP* 4.6 3.5 + + - -
232D THR* 3.5 25.2 + - - -
233D LEU* 3.7 15.7 - - + +
363D ARG* 1.3 70.0 - - - +
365D ASN* 1.3 55.2 - - - +
366D PRO* 3.0 28.5 - - + +
367D THR* 2.6 26.0 + - + +
368D GLY* 2.4 36.7 + - - -
369D THR* 2.8 19.9 + - - +
371D LEU* 4.6 2.4 - - + +
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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