Contacts of the strand formed by residues 347 - 351 (chain D) in PDB entry 3DLX
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 VAL 347 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226D SER* 3.7 26.7 - - - -
341D LEU 4.6 0.2 - - - -
342D GLN* 3.3 8.5 - - - +
343D SER* 2.7 49.3 + - - -
345D ASN* 4.3 4.7 - - - +
346D GLY* 1.3 82.8 - - - +
348D LEU* 1.3 66.2 + - - +
349D GLY 4.2 0.2 - - - -
350D LEU* 3.6 15.0 - - + +
363D LEU* 4.3 5.6 - - + -
364D ILE 4.4 2.2 - - - +
373D ILE* 3.6 31.9 - - + -
378D SER 3.5 5.4 - - - +
379D PHE* 3.8 11.2 - - + -
380D PHE* 3.6 4.4 - - - -
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Residues in contact with LEU 348 (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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262C PRO* 4.2 10.3 - - + -
263C GLN* 4.0 17.6 - - + +
264C ILE* 3.8 38.6 - - + +
318D TYR* 3.8 29.2 - - + -
340D HIS* 4.3 4.9 - - + +
341D LEU 3.7 3.6 - - - +
342D GLN* 3.7 31.4 - - + +
347D VAL* 1.3 74.1 - - - +
349D GLY* 1.3 62.5 + - - +
350D LEU 3.9 0.2 - - - -
376D GLY 4.7 0.2 - - - +
377D ALA* 3.2 8.7 - - - +
378D SER* 3.0 40.4 + - - +
380D PHE* 3.6 9.8 - - + -
388D MET* 4.9 1.6 - - - -
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Residues in contact with GLY 349 (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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263C GLN* 5.5 2.9 - - - -
340D HIS* 5.2 7.0 - - - -
341D LEU 2.8 19.7 + - - -
348D LEU* 1.3 78.8 - - - +
350D LEU* 1.3 64.7 + - - -
373D ILE* 3.5 5.7 - - - +
374D LEU* 2.9 33.1 + - - +
377D ALA* 3.9 8.8 - - - +
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Residues in contact with LEU 350 (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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321D LEU* 6.1 6.7 - - + -
327D LEU* 6.4 0.9 - - + -
339D VAL 5.4 0.9 - - - +
341D LEU* 3.2 42.6 + - + +
342D GLN 4.6 8.3 - - - +
343D SER* 3.9 25.4 - - - +
347D VAL* 3.6 28.0 - - + -
348D LEU 3.9 0.2 - - - -
349D GLY* 1.3 79.5 - - - +
351D GLY* 1.3 64.2 + - - +
363D LEU* 4.8 0.2 - - + -
364D ILE 4.9 0.4 - - - +
365D ASN* 4.4 13.7 - - + -
371D VAL* 3.6 32.5 - - + -
372D THR 3.5 4.7 - - - +
373D ILE* 4.5 0.7 - - + +
374D LEU* 3.5 11.4 - - - +
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Residues in contact with GLY 351 (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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330D SER* 5.5 2.1 + - - -
341D LEU* 5.9 1.9 - - - +
349D GLY 3.5 1.0 + - - -
350D LEU* 1.3 80.4 - - - +
352D PRO* 1.3 81.2 - - - +
371D VAL* 4.5 6.2 - - - +
372D THR* 2.7 24.8 + - - +
374D LEU* 3.7 14.1 - - - -
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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