Contacts of the helix formed by residues 562 - 570 (chain B) in PDB entry 1N1M
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 562 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B TYR* 3.9 5.5 - - - -
48B TYR* 3.5 20.3 - - + +
529B ILE* 4.9 5.1 - - - +
560B ARG* 3.4 37.2 - - + +
561B LEU* 1.3 74.8 - - - +
563B TRP* 1.3 67.0 + - + +
564B ALA* 2.8 39.4 + - - +
565B THR* 2.9 24.1 + - - -
566B TYR 3.5 2.8 + - - -
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Residues in contact with TRP 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 4.0 9.9 - - + -
48B TYR* 3.6 18.7 + + + +
543B LEU* 4.3 0.4 - - + -
562B ASN* 1.3 76.4 - - + +
564B ALA* 1.3 57.5 + - - +
566B TYR* 2.9 44.6 + + - +
567B LEU* 3.0 42.9 + - + +
627B TRP* 3.6 46.9 - + + -
651B ILE* 4.4 0.4 - - + -
752B TYR* 3.6 36.0 + + + -
755B MET* 3.9 24.5 - - + -
756B SER* 3.2 39.4 + - - -
759B ILE* 3.9 22.9 - - + -
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Residues in contact with ALA 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B ILE* 3.7 19.9 - - + +
545B ASP* 5.1 5.6 - - - +
562B ASN* 2.8 17.0 + - - +
563B TRP* 1.3 78.1 - - - +
565B THR* 1.3 63.4 + - - +
567B LEU* 3.9 4.8 - - - +
568B ALA* 3.1 26.5 + - - +
575B VAL* 3.7 37.4 - - + +
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Residues in contact with THR 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B TYR* 3.4 26.2 - - + -
509B MET* 4.5 2.9 - - + -
510B PRO* 3.7 32.0 - - + +
529B ILE* 4.9 4.7 - - - +
560B ARG 3.2 15.8 + - - +
561B LEU* 3.5 13.2 - - + -
562B ASN* 2.9 28.6 + - - -
564B ALA* 1.3 78.1 - - - +
566B TYR* 1.3 57.0 + - - +
569B SER* 2.9 33.4 + - - -
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Residues in contact with TYR 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B TYR* 3.7 24.6 - - + +
44B THR* 4.5 1.6 - - - +
45B LEU* 3.4 49.2 - - + +
48B TYR* 4.9 2.7 - - + -
562B ASN 3.5 3.0 + - - +
563B TRP* 2.9 38.5 + + + +
565B THR* 1.3 76.0 - - - +
567B LEU* 1.3 88.0 + - + +
568B ALA 3.0 1.6 - - - -
570B THR* 2.9 34.7 + - + -
571B GLU* 3.1 36.2 + - + +
756B SER* 3.8 9.9 - - - -
760B LYS* 3.7 15.6 + - + +
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Residues in contact with LEU 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B LEU* 3.6 31.0 - - + -
563B TRP* 3.0 46.3 + - + +
564B ALA* 3.3 6.9 + - - +
566B TYR* 1.3 102.0 - - + +
568B ALA* 1.3 50.4 + - - +
571B GLU* 3.4 9.8 - - + +
572B ASN 3.2 8.0 + - - -
573B ILE* 2.7 51.7 + - + +
575B VAL* 3.9 14.8 - - + -
756B SER* 5.4 1.8 - - - +
759B ILE* 4.6 7.9 - - + -
760B LYS* 6.4 0.4 - - + -
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Residues in contact with ALA 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B PRO* 3.8 19.1 - - + -
529B ILE* 3.7 19.7 - - + +
531B PRO* 3.4 7.6 - - - +
532B PRO* 3.4 14.2 - - - +
564B ALA 3.1 15.5 + - - +
565B THR 4.2 0.2 - - - +
566B TYR 3.0 0.4 - - - -
567B LEU* 1.3 78.1 - - - +
569B SER* 1.3 64.8 + - - +
570B THR 3.4 0.2 - - - -
572B ASN* 3.4 17.2 - - - -
573B ILE 3.2 19.3 - - - +
575B VAL* 4.9 0.4 - - + -
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Residues in contact with SER 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B THR* 3.2 19.6 - - - +
43B TYR* 2.4 43.6 + - - +
508B GLN 3.2 12.3 + - - -
510B PRO* 4.0 8.4 - - - +
532B PRO* 3.7 18.8 - - - +
565B THR 2.9 22.2 + - - -
568B ALA* 1.3 80.3 - - - +
570B THR* 1.3 57.3 + - - +
572B ASN* 4.7 4.3 + - - +
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Residues in contact with THR 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B THR* 2.8 22.9 + - + +
43B TYR 2.5 27.6 + - - -
44B THR* 3.8 8.9 - - + -
566B TYR* 2.9 22.1 + - + -
569B SER* 1.3 76.5 - - - +
571B GLU* 1.3 70.4 + - - +
572B ASN* 3.1 19.3 - - - +
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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