Contacts of the helix formed by residues 541 - 546 (chain I) in PDB entry 4XLN
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 SER 541 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405I ARG* 6.1 0.2 - - - -
408I ARG* 4.4 0.9 - - - -
439I CYS* 3.1 25.0 - - - +
442I GLU* 3.2 19.6 + - - -
454I SER* 3.8 13.0 - - - -
455I LEU 3.7 22.4 - - - -
456I ALA* 4.1 0.2 - - - +
457I ALA* 4.1 2.9 - - - +
540I PHE* 1.3 72.2 - - - +
542I LEU* 1.3 63.2 + - - +
543I ASN* 4.0 0.6 + - - -
544I THR* 3.5 16.8 + - - -
545I ASN* 2.8 31.5 + - - +
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Residues in contact with LEU 542 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I LEU* 5.7 1.8 - - + -
18I LEU* 3.7 20.9 - - + -
401I LEU* 4.5 12.3 - - + -
404I LEU* 3.7 42.8 - - + +
405I ARG* 4.7 2.9 - - + +
408I ARG* 3.3 42.4 - - - +
457I ALA* 4.7 9.2 - - + -
541I SER* 1.3 76.4 - - - +
543I ASN* 1.3 64.2 + - - +
545I ASN* 2.8 23.0 + - - +
546I LEU* 2.9 20.1 + - + +
583I LEU* 6.1 1.1 - - - -
587I VAL* 5.5 6.3 - - + -
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Residues in contact with ASN 543 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401I LEU* 3.6 23.2 + - - +
405I ARG* 3.1 42.0 - - - +
442I GLU* 3.2 18.2 - - - +
541I SER* 3.6 0.5 + - - -
542I LEU* 1.3 77.3 + - - +
544I THR* 1.3 62.8 + - - +
546I LEU* 3.1 19.8 + - - +
547I ILE* 3.4 12.1 - - - +
562I SER* 3.2 23.5 + - - +
565I GLN* 3.5 17.9 + - - +
566I THR* 3.6 12.9 + - - +
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Residues in contact with THR 544 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439I CYS* 3.5 12.4 - - - -
441I VAL* 3.5 26.3 - - + +
442I GLU* 3.7 3.8 - - - +
540I PHE* 3.5 21.8 - - + -
541I SER* 3.5 19.5 + - - -
542I LEU 3.2 0.4 - - - -
543I ASN* 1.3 78.3 - - - +
545I ASN* 1.3 61.8 + - - +
546I LEU 3.3 1.0 + - - -
547I ILE* 3.3 17.4 + - + +
550I LEU* 3.6 28.2 - - + +
558I ALA* 5.6 0.9 - - + -
562I SER* 3.5 21.7 + - - +
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Residues in contact with ASN 545 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457I ALA* 4.4 2.7 - - + +
537I LYS* 2.5 49.3 + - - +
540I PHE* 3.3 21.2 + - - +
541I SER 2.8 15.6 + - - +
542I LEU* 2.8 7.4 + - - +
544I THR* 1.3 75.6 - - - +
546I LEU* 1.3 51.6 + - - +
547I ILE 3.2 2.2 - - - -
581I THR* 2.7 35.4 + - - +
583I LEU* 3.2 25.9 - - + +
905I VAL* 3.2 28.7 - - - +
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Residues in contact with LEU 546 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401I LEU* 3.6 30.7 - - + -
542I LEU 2.9 16.7 + - - +
543I ASN* 3.1 10.6 + - - +
545I ASN* 1.3 76.5 - - - +
547I ILE* 1.3 61.0 + - - +
548I PRO* 3.4 10.8 - - - +
565I GLN* 3.5 21.1 - - - +
581I THR* 3.6 5.1 + - - +
583I LEU* 4.0 22.4 - - + -
584I GLU* 3.4 30.7 - - + +
587I VAL* 4.1 13.0 - - + -
666I LEU* 3.6 16.2 - - + -
842I ARG* 3.4 18.1 + - - -
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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