Contacts of the helix formed by residues 517 - 527 (chain A) in PDB entry 2JLF
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 ASN 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLY 5.2 1.0 - - - +
80A VAL* 6.1 0.5 - - - -
81A ARG* 3.4 38.6 + - - +
82A THR* 6.1 0.2 - - - +
498A GLY* 3.3 18.4 + - - +
500A ILE* 3.9 27.4 - - + +
516A GLY* 1.3 70.9 - - - -
518A ILE* 1.3 64.0 + - - +
519A ASN* 2.7 39.0 + - - +
520A SER* 3.1 36.6 + - - +
558A TYR* 3.4 12.3 - - - -
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Residues in contact with ILE 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLY 5.4 5.3 + - - +
80A VAL* 4.7 10.1 - - + -
84A PHE* 3.9 25.8 - - + -
516A GLY 3.4 4.8 + - - -
517A ASN* 1.3 72.1 + - - +
519A ASN* 1.3 71.5 + - + +
521A MET* 3.2 38.9 + - + +
522A LEU* 3.5 8.1 + - - +
558A TYR* 4.1 13.7 - - + -
561A CYS* 3.9 27.8 - - + -
563A ILE* 4.3 18.4 - - + -
564A TYR* 4.3 10.1 - - + -
567A VAL* 4.1 21.5 - - + -
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Residues in contact with ASN 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL* 4.9 2.4 - - - +
81A ARG* 5.2 2.6 - - - +
82A THR* 3.0 43.6 + - - +
83A ASN 3.2 10.1 + - - -
84A PHE* 2.9 37.2 - - - +
87A MET* 5.8 0.3 - - - +
517A ASN* 2.7 23.9 + - - +
518A ILE* 1.3 78.3 - - - +
520A SER* 1.3 60.3 + - - +
522A LEU* 3.2 8.0 + - - +
523A ASN* 2.9 34.5 + - - +
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Residues in contact with SER 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A GLY* 4.5 7.2 + - - -
517A ASN* 3.1 34.8 + - - +
518A ILE 3.2 0.4 - - - -
519A ASN* 1.3 78.6 - - - +
521A MET* 1.3 61.6 + - - +
523A ASN* 3.1 12.5 + - - +
524A ASN* 2.9 29.4 + - - +
558A TYR* 3.6 12.3 - - - -
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Residues in contact with MET 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A ASN 3.8 0.4 + - - -
518A ILE* 3.2 24.1 + - + +
520A SER* 1.3 77.9 - - - +
522A LEU* 1.3 67.2 + - + +
524A ASN* 3.1 5.5 + - - +
525A GLN* 2.9 44.1 + - + +
554A MET* 3.6 25.4 - - - +
558A TYR* 3.4 55.5 + - + -
564A TYR* 4.6 3.4 - - + -
567A VAL* 4.0 12.6 - - + -
568A LEU* 4.7 7.9 - - + -
571A ILE* 3.9 28.7 - - + -
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Residues in contact with LEU 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 4.5 5.8 - - + -
61A LEU* 3.7 12.6 - - + -
84A PHE* 3.4 36.6 - - + -
87A MET* 3.6 25.9 - - + +
518A ILE 3.7 13.5 - - - +
519A ASN* 3.2 9.8 + - - +
521A MET* 1.3 78.1 - - + +
523A ASN* 1.3 63.3 + - - +
526A PHE* 3.1 42.5 + - + +
527A SER* 3.8 1.0 + - - -
567A VAL* 3.9 10.3 - - + -
571A ILE* 3.5 35.0 - - + -
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Residues in contact with ASN 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLY* 5.3 1.9 - - - -
87A MET* 5.2 5.8 + - - +
208A THR* 3.2 46.3 + - + +
519A ASN* 2.9 25.7 + - - +
520A SER* 3.3 11.1 - - - +
521A MET 3.1 0.4 - - - -
522A LEU* 1.3 78.1 - - - +
524A ASN* 1.3 66.3 + - - +
527A SER* 2.8 40.2 + - - +
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Residues in contact with ASN 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR* 4.1 3.8 + - - -
520A SER* 2.9 18.0 + - - +
521A MET* 3.6 8.5 - - - +
523A ASN* 1.3 78.8 - - - +
525A GLN* 1.3 63.1 + - + +
526A PHE 3.7 0.2 + - - -
527A SER 4.9 0.9 - - - -
528A PRO* 4.1 16.2 - - - +
544A ARG* 4.4 6.1 + - - -
558A TYR* 3.8 15.2 + - + +
620A GLU* 4.3 7.1 + - - -
624A ASP* 5.9 0.2 - - - -
627A LYS* 3.4 32.8 - - - +
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Residues in contact with GLN 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR* 4.7 0.2 - - - +
40A TYR* 2.7 34.8 + - - -
521A MET* 2.9 35.7 + - + +
524A ASN* 1.3 80.5 - - + +
526A PHE* 1.3 78.9 + - + +
528A PRO* 5.0 1.3 - - - -
550A ALA* 6.3 1.8 - - + -
551A TRP* 3.8 9.0 - - - +
554A MET* 3.4 32.3 - - - +
558A TYR* 5.6 0.4 - - - -
568A LEU* 5.9 0.2 - - - +
571A ILE* 4.9 2.6 - - - +
583A TYR* 2.5 38.1 + - - +
587A ARG* 3.7 15.9 - - - +
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Residues in contact with PHE 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR* 4.5 0.7 - - - -
40A TYR* 5.0 1.3 - + - -
50A PHE* 3.0 41.6 - + + -
53A PHE* 3.7 34.3 - + + -
54A LYS* 3.2 19.4 + - + -
57A LEU* 4.5 3.1 - - + -
87A MET* 5.1 6.5 - - + -
91A ASN* 3.5 0.7 - - - +
522A LEU* 3.1 47.5 + - + +
525A GLN* 1.3 95.1 - - + +
527A SER* 1.3 62.8 + - - +
528A PRO* 3.3 10.6 - - - +
571A ILE* 4.0 13.9 - - + -
575A TRP* 3.9 4.3 - + - -
583A TYR* 3.4 42.8 - + - -
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Residues in contact with SER 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 3.5 8.3 + - - -
87A MET* 3.6 22.2 + - - +
91A ASN* 3.5 20.0 + - - -
207A SER* 2.8 25.4 + - - -
208A THR* 4.2 16.8 - - - -
522A LEU 3.8 1.2 + - - -
523A ASN* 2.8 23.3 + - - +
526A PHE* 1.3 83.5 + - - +
528A PRO* 1.3 60.1 - - - +
529A GLU 3.9 0.3 + - - -
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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