Contacts of the strand formed by residues 410 - 415 (chain B) in PDB entry 4LT6
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 ILE 410 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B LEU* 3.2 60.3 - - + +
405B GLU* 4.0 9.6 - - - +
407B ASN* 3.5 31.0 + - + +
408B GLU 3.5 2.4 - - - +
409B PHE* 1.3 78.3 - - - +
411B THR* 1.3 64.6 + - - +
412B LEU 3.9 21.8 - - - +
413B ALA* 5.0 0.4 - - + -
440B ILE* 4.2 9.2 - - + -
441B ILE 3.8 4.0 - - - +
442B PHE* 3.7 21.5 - - + -
443B ARG* 5.0 1.2 - - - +
455B LEU* 3.6 19.3 - - + -
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Residues in contact with THR 411 (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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31A LYS* 5.1 5.5 + - - -
330B THR* 4.8 7.4 + - - -
331B SER* 4.1 4.2 + - - -
405B GLU* 5.7 5.0 - - - +
410B ILE* 1.3 76.4 - - - +
412B LEU* 1.3 65.6 + - + +
441B ILE* 3.2 24.1 + - + -
442B PHE 4.0 6.4 + - - -
443B ARG* 3.6 23.4 - - - +
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B SER* 3.3 21.8 - - - +
334B THR* 3.6 37.2 - - + -
335B VAL* 4.4 5.4 - - + -
370B TYR* 3.8 24.2 - - + +
405B GLU* 5.7 0.7 - - - -
410B ILE* 3.8 6.7 - - - +
411B THR* 1.3 85.2 - - + +
413B ALA* 1.3 62.0 + - - +
414B HIS* 3.7 28.5 - - + +
439B GLY 4.8 0.7 - - - +
440B ILE* 3.4 6.1 - - - -
441B ILE* 3.2 45.9 + - + +
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Residues in contact with ALA 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B SER* 2.8 29.3 + - - +
332B THR* 4.8 3.3 + - - +
401B VAL* 3.7 30.7 - - + +
404B LEU* 4.0 35.0 - - + -
405B GLU* 4.4 4.4 - - + +
410B ILE* 5.0 0.4 - - + -
412B LEU* 1.3 74.5 - - - +
414B HIS* 1.3 60.6 + - - +
415B VAL 4.1 1.0 + - - -
438B LEU* 4.9 2.9 - - + -
439B GLY 3.5 6.1 - - - +
440B ILE* 4.7 1.3 - - + -
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Residues in contact with HIS 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG 5.9 1.2 + - - -
234B GLY 5.0 4.4 + - - -
235B ILE* 5.7 0.2 - - - +
242B PHE* 4.0 15.2 - + - -
332B THR* 5.7 2.0 - - - -
335B VAL* 3.4 34.9 - - + +
339B GLU* 5.9 1.1 - - - -
366B PHE* 3.7 23.7 - + - -
369B LYS* 5.3 6.1 - - + -
370B TYR* 2.5 40.2 + + + +
412B LEU* 3.7 11.0 - - + -
413B ALA* 1.3 75.1 - - - +
415B VAL* 1.3 77.5 + - - +
416B ASN* 5.2 1.0 - - - -
417B PRO* 5.5 0.2 - - - +
437B PHE 3.7 1.0 - - - +
438B LEU* 3.3 6.3 - - - +
439B GLY 2.9 34.0 + - - +
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Residues in contact with VAL 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 3.8 32.5 - - + +
242B PHE* 3.6 12.0 - - + -
332B THR* 5.1 4.0 - - + +
397B ILE* 3.4 34.5 - - + -
401B VAL* 3.8 20.2 - - + -
413B ALA 4.1 0.4 - - - -
414B HIS* 1.3 86.2 - - - +
416B ASN* 1.3 66.7 + - - +
417B PRO* 3.2 11.1 - - - +
436B TRP* 5.5 2.5 - - + -
437B PHE 3.6 4.0 - - - +
438B LEU* 3.6 23.6 - - + +
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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