Contacts of the helix formed by residues 583 - 591 (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 LEU 583 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11I GLU* 6.0 0.2 - - - +
15I LEU* 5.9 6.3 - - + -
457I ALA* 5.9 4.0 - - + -
537I LYS* 3.2 39.9 - - + +
542I LEU* 5.4 1.3 - - - +
545I ASN* 3.2 39.9 - - + +
546I LEU* 4.0 15.5 - - + -
581I THR* 3.4 13.9 + - - +
582I GLY* 1.3 78.5 - - - +
584I GLU* 1.3 62.2 + - - +
585I GLU* 3.1 7.7 + - - -
586I ARG* 3.4 13.7 + - - +
587I VAL* 3.2 17.2 + - + +
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Residues in contact with GLU 584 (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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546I LEU* 3.4 31.0 - - + +
577I PRO* 4.7 3.3 - - + +
580I MET* 3.3 43.3 - - + +
581I THR* 3.6 8.5 + - - -
582I GLY 3.0 21.4 + - - -
583I LEU* 1.3 76.5 + - - +
585I GLU* 1.3 66.7 + - - +
587I VAL* 3.6 17.9 + - - +
588I VAL 3.7 2.6 + - - -
664I GLY 3.5 4.4 - - - +
665I PHE* 4.2 1.1 - - - -
666I LEU* 3.3 51.3 + - + +
842I ARG* 4.5 2.4 + - - -
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Residues in contact with GLU 585 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I ARG* 5.7 2.3 + - - -
580I MET* 5.3 1.6 - - + -
582I GLY* 4.1 15.5 - - - +
584I GLU* 1.3 81.1 - - - +
586I ARG* 1.3 64.4 + - - +
588I VAL* 3.3 17.7 - - - +
589I ARG* 3.7 19.2 + - - +
664I GLY 3.5 10.6 - - - +
665I PHE* 3.5 31.7 - - + -
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Residues in contact with ARG 586 (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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14I PRO* 3.3 26.3 - - - +
15I LEU* 2.4 52.5 + - + +
18I LEU* 4.7 7.2 - - + -
583I LEU* 3.4 8.0 + - - +
585I GLU* 1.3 78.1 - - + +
587I VAL* 1.3 65.8 + - - +
589I ARG* 3.1 20.1 + - - +
590I ASP* 2.9 53.4 + - - +
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Residues in contact with VAL 587 (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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18I LEU* 6.0 2.0 - - - -
400I PRO* 6.0 0.2 - - + -
401I LEU* 3.7 20.4 - - + +
404I LEU* 3.6 14.6 - - + +
542I LEU* 5.5 6.3 - - + -
546I LEU* 4.1 19.5 - - + -
583I LEU* 3.2 19.3 - - + +
584I GLU* 3.6 16.6 - - - +
585I GLU 3.2 0.8 - - - -
586I ARG* 1.3 77.4 - - + +
588I VAL* 1.3 64.6 + - - +
590I ASP* 5.3 0.2 - - - -
591I SER* 3.1 26.5 + - - -
666I LEU* 3.6 31.9 - - + -
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Residues in contact with VAL 588 (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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400I PRO* 5.5 4.0 - - + -
585I GLU 3.3 5.6 + - - +
587I VAL* 1.3 75.9 - - - +
589I ARG* 1.3 60.3 + - - +
591I SER* 2.8 19.4 + - - +
592I LEU 3.7 3.1 + - - -
593I ALA* 3.8 7.9 + - + -
594I ALA* 4.1 9.3 + - + +
596I TYR* 3.2 20.1 + - - +
660I ALA 5.1 0.2 - - - -
661I SER* 3.8 25.1 - - - +
664I GLY* 3.2 32.3 - - - +
665I PHE 3.9 0.2 - - - -
666I LEU* 3.7 42.6 - - + +
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Residues in contact with ARG 589 (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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585I GLU* 3.9 21.2 + - - +
586I ARG* 3.1 25.8 + - - +
587I VAL 3.1 0.6 - - - -
588I VAL* 1.3 77.6 - - - +
590I ASP* 1.3 64.8 + - - +
591I SER 3.0 4.0 - - - -
592I LEU* 2.7 38.1 + - + +
596I TYR* 3.2 50.0 - - + +
652I GLY* 3.5 17.4 + - - -
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Residues in contact with ASP 590 (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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16I PRO 4.1 0.7 - - - +
17I PRO* 3.2 24.3 - - + +
18I LEU* 3.2 40.7 - - + +
19I THR* 3.4 28.2 + - - +
404I LEU* 3.7 5.1 - - + +
586I ARG* 2.9 42.3 + - - +
587I VAL 4.4 0.9 - - - +
589I ARG* 1.3 78.8 - - - +
591I SER* 1.3 60.1 + - - +
592I LEU* 3.2 11.0 - - - +
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Residues in contact with SER 591 (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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19I THR* 5.4 0.4 - - - -
124I ASP* 4.3 10.9 - - - +
400I PRO* 3.7 36.1 - - - +
403I SER* 5.5 3.1 + - - -
404I LEU* 4.1 13.9 - - - +
587I VAL* 3.1 14.2 + - - -
588I VAL* 2.8 30.3 + - - -
590I ASP* 1.3 76.0 - - - +
592I LEU* 1.3 67.7 + - - +
593I ALA* 3.1 9.0 + - - +
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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