Contacts of the strand formed by residues 436 - 440 (chain C) 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 LYS 436 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C GLU* 2.6 29.6 + - - -
395C ASP 3.1 16.4 + - - +
396C LEU* 3.3 15.8 - - + +
397C THR 2.9 26.3 + - - +
434C LYS 4.2 0.8 + - - -
435C THR* 1.3 71.4 - - - +
437C VAL* 1.3 61.9 + - - +
438C VAL* 3.8 17.9 - - + -
467C ASN* 3.3 19.5 - - + -
468C ARG* 3.6 28.0 - - - +
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Residues in contact with VAL 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C THR* 3.3 11.0 - - - +
399C LEU* 4.9 8.3 - - + -
410C LEU* 5.0 0.7 - - + -
429C LEU 4.3 7.2 - - - +
430C VAL* 4.1 40.4 - - + -
432C SER 5.4 1.3 - - - +
435C THR 3.9 9.9 - - - +
436C LYS* 1.3 75.9 - - - +
438C VAL* 1.3 69.6 + - - +
439C VAL* 4.6 4.9 - - + -
465C CYS 3.4 25.4 - - - +
466C VAL* 3.8 16.6 - - + +
467C ASN* 2.8 36.9 + - - +
468C ARG 3.3 6.9 + - - +
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Residues in contact with VAL 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLU* 4.1 7.0 - - + +
396C LEU* 3.3 30.1 - - + -
397C THR 2.9 6.4 + - - +
398C MET* 3.2 21.6 - - + +
399C LEU* 2.9 25.3 + - - +
436C LYS* 3.8 20.9 - - + -
437C VAL* 1.3 78.8 - - - +
439C VAL* 1.3 68.7 + - - +
440C THR* 4.5 1.3 - - + -
468C ARG* 3.4 16.2 - - + +
470C ILE* 3.7 31.6 - - + -
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Residues in contact with VAL 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C LEU* 3.2 11.9 - - + +
401C ALA* 3.6 24.0 - - + -
404C VAL* 3.8 12.6 - - + -
410C LEU* 3.8 20.6 - - + -
437C VAL* 4.1 3.8 - - + -
438C VAL* 1.3 74.9 - - - +
440C THR* 1.3 64.1 + - - +
441C MET* 4.0 17.7 - - + -
466C VAL* 3.8 32.8 - - + -
468C ARG 3.0 11.0 + - - +
469C ILE* 3.5 4.5 - - + -
470C ILE 2.8 27.5 + - - +
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Residues in contact with THR 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C ILE* 3.7 18.4 - - + -
309C ALA* 3.7 29.8 - - + -
325C ILE* 4.0 16.9 - - + +
326C PRO* 3.5 29.3 - - + +
398C MET* 3.8 17.4 - - + +
399C LEU 2.9 5.3 + - - -
400C GLY* 3.7 14.4 - - - -
438C VAL* 4.5 0.7 - - + -
439C VAL* 1.3 77.0 - - - +
441C MET* 1.3 61.4 + - - +
470C ILE* 3.4 15.3 - - + -
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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