Contacts of the strand formed by residues 390 - 394 (chain B) in PDB entry 3L5J
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 ALA 390 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307B ALA* 3.6 10.2 - - + +
308B PRO 3.6 16.2 - - - +
310B PHE* 3.5 34.9 - - + -
376B ALA 3.9 0.2 - - - +
377B THR* 3.0 10.0 - - - -
378B LEU* 2.9 37.4 + - + +
389B ALA* 1.3 72.5 - - - +
391B VAL* 1.3 58.8 + - - +
430B LYS* 5.8 1.8 - - - +
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Residues in contact with VAL 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LEU* 3.6 25.6 - - + -
376B ALA 3.5 1.3 - - - -
377B THR* 3.9 17.7 - - + -
389B ALA* 3.8 13.3 + - + +
390B ALA* 1.3 78.5 - - - +
392B LEU* 1.3 71.9 + - - +
393B THR* 5.2 1.8 - - - +
430B LYS* 4.8 8.3 + - - +
477B VAL* 5.7 2.8 - - - +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B PHE* 3.2 57.9 - - + +
311B TRP* 3.4 37.5 - - + +
312B TYR* 3.5 28.9 - - + -
327B LEU* 4.7 3.4 - - + -
375B LEU* 3.1 12.7 - - - +
376B ALA* 2.7 34.2 + - + +
390B ALA 4.2 0.2 - - - -
391B VAL* 1.3 76.7 - - - +
393B THR* 1.3 62.6 + - - +
394B ILE* 4.1 2.5 - - + -
430B LYS* 3.5 14.1 - - - +
477B VAL* 5.7 2.9 - - + -
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Residues in contact with THR 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TYR* 3.7 9.1 + - - -
373B ARG* 3.8 32.8 - - + -
374B TYR 3.3 5.6 - - - +
375B LEU* 4.0 10.7 - - - +
391B VAL* 5.2 1.9 - - - +
392B LEU* 1.3 80.7 + - - +
394B ILE* 1.3 64.1 + - - +
395B PRO* 3.0 21.7 - - + +
479B ALA 5.6 0.9 + - - -
480B ASP 4.6 17.1 + - - +
481B GLY* 4.9 8.1 - - - -
482B PRO* 4.1 7.5 - - + +
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Residues in contact with ILE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B TYR* 4.6 20.2 - - + -
314B ILE* 5.2 5.2 - - + -
323B ARG* 3.5 30.7 - - - +
325B VAL* 4.5 23.1 - - + -
327B LEU* 4.5 12.1 - - + -
348B LEU* 4.9 3.1 - - + -
369B LEU* 4.7 5.4 - - + -
373B ARG* 3.3 2.1 - - - +
374B TYR* 2.8 54.2 + - + +
376B ALA* 3.8 29.6 - - + +
392B LEU* 4.7 6.3 - - + -
393B THR* 1.3 72.4 - - - +
395B PRO* 1.3 69.0 - - + +
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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