Contacts of the helix formed by residues 529 - 539 (chain A) in PDB entry 2N5T
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 529 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507A GLY* 3.9 22.0 + - - -
525A MET* 3.5 15.7 - - - -
526A SER* 3.0 17.1 + - - -
527A ALA 2.8 0.2 + - - -
528A ILE* 1.3 87.2 - - - +
530A ILE* 1.3 67.3 + - - +
531A PRO 3.4 1.1 - - - -
532A ARG* 3.3 13.9 + - - +
533A ILE* 3.2 22.6 + - - +
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Residues in contact with ILE 530 (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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271A VAL* 3.6 19.0 - - + +
272A CYS* 3.7 19.1 - - - +
273A ALA* 3.9 0.9 - - + +
287A ASN* 3.1 20.4 - - + +
288A GLY 4.1 12.1 - - - +
289A ALA* 3.6 31.0 - - + +
525A MET* 3.6 23.3 - - + -
526A SER 3.9 0.2 - - - +
527A ALA* 2.8 31.9 + - + +
529A SER* 1.3 78.0 - - - +
531A PRO* 1.4 58.7 - - - +
533A ILE* 3.9 1.2 - - - +
534A LYS* 2.8 38.3 + - - +
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Residues in contact with PRO 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.7 41.7 - - + +
287A ASN* 3.8 27.8 - - + +
527A ALA 3.7 4.3 - - - +
528A ILE 3.7 11.9 - - - +
529A SER 3.6 2.2 - - - -
530A ILE* 1.4 94.1 - - + +
532A ARG* 1.3 56.1 + - - +
534A LYS* 3.6 9.7 - - + +
535A LYS* 2.8 31.9 + - - +
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Residues in contact with ARG 532 (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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253A LEU* 4.4 30.0 - - + +
507A GLY 5.9 1.8 - - - +
509A GLU* 3.4 40.1 + - + +
528A ILE 5.1 6.5 + - - +
529A SER* 3.3 15.7 + - - +
531A PRO* 1.3 77.0 - - - +
533A ILE* 1.3 64.9 + - + +
535A LYS* 3.3 8.9 + - - +
536A ILE* 3.1 28.5 + - + +
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Residues in contact with ILE 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL* 5.1 2.7 - - + -
506A ALA 3.5 5.8 - - - +
507A GLY 3.5 30.3 - - - +
508A ASP 3.8 7.0 - - - -
509A GLU* 3.9 7.9 - - + +
512A THR* 2.9 35.2 - - + +
523A PHE* 4.5 4.7 - - + -
525A MET* 3.8 29.4 - - + -
529A SER 3.2 16.8 + - - +
530A ILE 3.9 2.2 - - - +
531A PRO 3.2 0.2 - - - -
532A ARG* 1.3 77.6 - - + +
534A LYS* 1.3 66.1 + - - +
536A ILE* 3.1 6.5 + - + +
537A ILE* 2.9 47.4 + - + +
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Residues in contact with LYS 534 (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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256A LEU* 3.2 33.0 + - + +
257A LYS* 4.1 19.4 + - - +
260A PRO* 5.7 1.2 - - - +
261A ALA* 4.7 14.8 - - + +
271A VAL* 5.2 4.9 - - + +
287A ASN 4.8 1.4 + - - -
288A GLY* 3.5 32.5 + - - -
290A GLU* 4.3 13.7 + - - +
530A ILE* 2.8 27.3 + - + +
531A PRO* 3.6 9.2 - - + +
533A ILE* 1.3 76.7 - - - +
535A LYS* 1.3 51.6 + - - +
537A ILE* 2.8 12.6 + - - +
538A ARG* 2.7 58.7 + - + +
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Residues in contact with LYS 535 (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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252A GLU* 6.0 4.2 - - - +
253A LEU* 6.2 3.8 - - + -
256A LEU* 5.1 10.8 - - + -
531A PRO 2.8 20.4 + - - +
532A ARG* 3.4 9.0 - - - +
533A ILE 3.1 0.2 - - - -
534A LYS* 1.3 75.0 - - - +
536A ILE* 1.3 64.2 + - + +
538A ARG* 3.4 5.6 + - - +
539A ASN* 2.8 46.5 + - - +
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Residues in contact with ILE 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A GLU* 3.6 48.0 - - + +
512A THR* 3.5 27.4 - - + +
513A LEU* 3.9 22.7 - - + -
532A ARG* 3.1 16.6 + - + +
533A ILE* 3.1 6.9 + - - +
535A LYS* 1.3 78.1 - - + +
537A ILE* 1.3 57.6 + - - +
539A ASN* 3.4 4.4 + - - +
540A THR* 2.7 33.5 + - - +
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Residues in contact with ILE 537 (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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261A ALA* 3.8 32.3 - - + +
263A THR* 3.2 37.6 - - + +
269A VAL* 3.8 25.1 - - + -
271A VAL* 4.1 12.3 - - + -
512A THR* 3.8 15.7 - - + -
516A LEU* 4.7 11.9 - - + -
523A PHE* 4.4 9.4 - - + -
533A ILE* 2.9 36.8 + - + +
534A LYS 2.8 7.2 + - - +
536A ILE* 1.3 77.7 - - - +
538A ARG* 1.3 65.3 + - - +
539A ASN 3.0 1.9 + - - -
540A THR* 3.3 8.7 + - - -
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Residues in contact with ARG 538 (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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256A LEU* 3.5 29.0 - - + +
257A LYS 4.3 0.2 + - - -
258A ASP* 2.6 41.5 + - - +
259A LEU* 3.2 26.5 + - - +
261A ALA* 4.6 0.9 - - - -
262A ILE* 3.3 32.8 + - - +
264A LEU* 3.5 26.3 + - - +
534A LYS* 2.7 36.4 + - + +
535A LYS* 3.9 5.2 - - - +
537A ILE* 1.3 77.0 - - - +
539A ASN* 1.3 63.8 + - - +
540A THR 3.6 0.7 - - - -
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Residues in contact with ASN 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 3.5 21.5 - - + +
535A LYS* 2.8 45.2 + - - +
536A ILE* 3.4 6.0 + - - +
537A ILE 3.1 0.8 - - - -
538A ARG* 1.3 85.6 - - - +
540A THR* 1.3 61.1 + - - +
572A LYS 4.5 1.9 - - - +
573A THR* 3.1 37.2 + - + +
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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