Contacts of the helix formed by residues 557 - 573 (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 THR 557 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A PRO* 3.6 5.1 - - - +
555A GLN* 3.2 3.9 + - - +
556A PRO* 1.3 91.2 + - - +
558A THR* 1.3 65.0 + - - +
559A ASP* 3.3 19.7 - - + +
560A GLU* 3.3 28.2 + - + +
561A LEU* 3.2 21.5 + - - +
396B VAL* 4.0 12.6 - - - +
397B GLU* 2.7 31.7 + - + +
400B ARG* 4.3 10.9 + - - +
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Residues in contact with THR 558 (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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475A GLN* 4.8 17.8 - - + +
477A MET* 3.1 28.0 + - + +
478A SER* 3.8 6.2 + - - -
479A PRO* 3.7 12.4 - - - +
557A THR* 1.3 68.0 - - - +
559A ASP* 1.3 71.2 + - - +
561A LEU* 2.8 12.2 + - + +
562A MET* 2.7 37.4 + - + +
397B GLU* 2.7 17.6 + - - -
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Residues in contact with ASP 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A THR* 3.3 13.3 - - + +
558A THR* 1.3 81.7 - - - +
560A GLU* 1.3 57.7 + - + +
562A MET* 3.1 10.7 + - - +
563A THR* 2.9 31.5 + - - -
397B GLU* 4.0 5.1 + - - +
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Residues in contact with GLU 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A GLN* 3.3 26.6 + - + +
556A PRO* 3.2 27.9 - - - +
557A THR* 3.3 27.1 + - + +
558A THR 3.1 0.4 - - - -
559A ASP* 1.3 76.7 - - + +
561A LEU* 1.3 61.9 + - - +
563A THR* 3.4 21.0 - - - -
564A LEU* 3.5 15.1 + - - +
400B ARG* 4.9 6.9 + - - -
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Residues in contact with LEU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A MET* 3.5 37.5 - - + +
479A PRO* 4.0 28.5 - - + -
482A LEU* 3.6 30.5 - - + -
514A LEU* 5.0 2.5 - - + -
552A ALA* 3.4 29.0 - - + +
555A GLN* 3.9 13.7 - - + +
557A THR 3.2 6.0 + - - +
558A THR* 2.8 15.0 + - + +
560A GLU* 1.3 78.0 - - - +
562A MET* 1.3 65.1 + - + +
563A THR 3.2 0.2 - - - -
564A LEU* 3.4 7.5 + - - +
565A VAL* 3.3 24.8 + - - +
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Residues in contact with MET 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A MET* 3.6 35.0 - - - +
510A ARG* 4.3 25.8 - - + +
558A THR* 2.7 34.2 + - + +
559A ASP* 3.4 13.0 - - - +
561A LEU* 1.3 74.7 - - + +
563A THR* 1.3 64.2 + - - +
565A VAL* 3.4 11.7 + - + +
566A ASN* 3.0 44.5 + - - +
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Residues in contact with THR 563 (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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559A ASP 2.9 14.8 + - - -
560A GLU* 3.4 12.9 - - - -
561A LEU 3.2 0.6 - - - -
562A MET* 1.3 76.2 - - - +
564A LEU* 1.3 62.8 + - + +
566A ASN* 3.1 9.5 + - + +
567A LYS* 2.9 53.0 + - + +
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Residues in contact with LEU 564 (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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548A LEU* 3.7 15.5 - - + +
551A GLN* 3.0 45.8 - - + +
552A ALA* 4.6 5.2 - - + +
555A GLN* 3.8 28.7 - - + +
560A GLU 3.5 21.2 + - - +
561A LEU* 3.4 8.9 + - - +
562A MET 3.3 0.2 - - - -
563A THR* 1.3 78.4 - - + +
565A VAL* 1.3 65.7 + - + +
567A LYS* 3.2 10.3 + - + +
568A PHE* 3.0 23.6 + - - +
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Residues in contact with VAL 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A MET* 5.0 3.8 - - + -
510A ARG* 4.0 22.7 - - + +
513A LEU* 4.6 8.2 - - + +
514A LEU* 3.9 39.3 - - + -
548A LEU* 3.8 10.5 - - + +
561A LEU 3.3 14.7 + - - +
562A MET* 3.5 16.6 - - + +
564A LEU* 1.3 79.2 - - + +
566A ASN* 1.3 68.0 + - - +
568A PHE* 3.1 6.0 - - - +
569A ILE* 3.0 40.4 + - + +
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Residues in contact with ASN 566 (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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562A MET* 3.0 35.5 + - - +
563A THR* 3.1 10.0 + - + +
565A VAL* 1.3 78.4 - - - +
567A LYS* 1.3 66.4 + - + +
568A PHE 3.0 1.8 - - - -
569A ILE* 3.1 14.1 + - - +
570A GLU* 3.0 32.4 + - + +
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Residues in contact with LYS 567 (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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563A THR* 2.9 43.9 + - + +
564A LEU* 3.9 9.4 - - + +
566A ASN* 1.3 73.4 - - + +
568A PHE* 1.3 61.1 + - - +
570A GLU* 3.4 22.4 - - - +
571A GLU* 3.0 30.1 + - - +
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Residues in contact with PHE 568 (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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513A LEU* 3.3 36.3 - - + -
540A THR* 4.4 8.5 - - + -
541A ASN 5.6 0.4 - - - -
544A ASP* 3.5 45.1 - - + -
545A ALA* 3.7 12.3 - - - -
548A LEU* 3.7 26.5 - - + -
564A LEU 3.0 12.0 + - - +
565A VAL* 3.1 12.1 - - - +
567A LYS* 1.3 76.6 - - - +
569A ILE* 1.3 57.1 + - - +
571A GLU* 2.9 2.3 + - - -
572A LYS* 2.7 70.5 + - + +
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Residues in contact with ILE 569 (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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509A GLU 5.5 6.7 - - - +
510A ARG* 6.1 1.1 - - - -
513A LEU* 4.1 16.8 - - + -
565A VAL* 3.0 30.8 + - + +
566A ASN* 3.1 14.6 + - - +
568A PHE* 1.3 80.7 - - - +
570A GLU* 1.3 63.9 + - + +
572A LYS* 5.2 0.2 - - - -
573A THR* 3.5 28.1 + - - +
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Residues in contact with GLU 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A ASN* 3.0 21.8 + - + +
567A LYS* 3.4 26.6 - - - +
569A ILE* 1.3 79.5 - - + +
571A GLU* 1.3 63.8 + - + +
573A THR 4.5 5.0 + - - -
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Residues in contact with GLU 571 (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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567A LYS* 3.0 16.1 + - - +
568A PHE 2.9 1.8 + - - -
570A GLU* 1.3 80.0 - - + +
572A LYS* 1.3 87.0 + - + +
573A THR 3.9 0.4 - - - -
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Residues in contact with LYS 572 (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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264A LEU* 6.0 0.5 - - - +
539A ASN 4.5 2.1 - - - +
544A ASP* 4.1 26.2 - - - +
567A LYS 5.2 0.2 + - - -
568A PHE* 2.7 65.2 + - + +
569A ILE* 5.2 0.2 - - - -
571A GLU* 1.3 110.2 + - + +
573A THR* 1.3 70.3 + - - +
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Residues in contact with THR 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 5.7 1.1 - - + +
539A ASN* 3.1 38.8 + - + +
540A THR* 5.2 0.2 - - - -
569A ILE* 3.5 23.8 + - - +
570A GLU 4.9 3.8 - - - -
571A GLU 3.9 0.8 - - - -
572A LYS* 1.3 92.3 + - - +
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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