Contacts of the helix formed by residues 562 - 570 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A TYR* 3.8 5.4 + - - -
48A TYR* 3.6 21.2 - - + +
545A ASP* 5.8 1.8 + - - -
560A ARG* 3.9 31.1 - - + +
561A LEU* 1.3 75.9 - - - +
563A TRP* 1.3 70.2 + - + +
564A ALA* 3.3 15.6 + - - +
565A THR* 2.8 41.7 + - - -
566A TYR* 3.4 2.8 + - - +
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Residues in contact with TRP 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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45A LEU* 4.1 10.8 - - + -
48A TYR* 3.7 14.4 + + + -
543A LEU* 4.3 0.4 - - + -
562A ASN* 1.3 77.0 - - + +
564A ALA* 1.3 62.8 - - - +
566A TYR* 2.9 33.7 + + - +
567A LEU* 3.0 46.3 + - + +
627A TRP* 3.6 51.8 - + + -
651A ILE* 4.4 2.9 - - + -
752A TYR* 3.4 39.7 - + + +
755A MET* 3.8 28.9 - - + -
756A SER* 3.2 27.7 + - - -
759A ILE* 3.8 22.2 - - + -
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Residues in contact with ALA 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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529A ILE* 4.2 14.7 - - + +
545A ASP* 5.0 7.0 - - - +
562A ASN* 3.2 16.4 + - - +
563A TRP* 1.3 78.5 - - - +
565A THR* 1.3 64.3 + - - +
567A LEU* 3.4 7.7 + - - +
568A ALA* 3.2 24.4 + - - +
575A VAL* 3.8 36.7 - - + +
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Residues in contact with THR 565 (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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43A TYR* 3.3 30.3 - - + -
509A MET* 4.3 12.6 - - + -
510A PRO* 3.9 29.4 - - + +
529A ILE* 4.7 3.3 - - - +
560A ARG 3.5 6.6 + - - +
561A LEU* 3.4 10.4 - - + -
562A ASN* 2.8 37.0 + - - -
564A ALA* 1.3 79.1 - - - +
566A TYR* 1.3 55.2 + - - +
568A ALA* 3.9 0.2 - - - -
569A SER* 2.8 32.1 + - - -
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Residues in contact with TYR 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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43A TYR* 3.5 22.8 - - + +
44A THR* 3.6 6.3 - - - +
45A LEU* 3.2 40.0 - - + +
48A TYR* 5.0 2.2 - - + -
562A ASN 3.4 1.2 + - - +
563A TRP* 2.9 28.1 + + + +
565A THR* 1.3 77.9 - - - +
567A LEU* 1.3 85.8 + - + +
570A THR* 2.7 54.5 + - + -
571A GLU* 2.7 31.2 + - + +
756A SER* 3.8 21.2 - - - -
760A LYS* 3.9 14.2 + - - +
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Residues in contact with LEU 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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543A LEU* 3.8 24.2 - - + -
563A TRP* 3.0 55.7 + - + +
564A ALA* 3.7 13.9 - - - +
566A TYR* 1.3 95.5 - - + +
568A ALA* 1.3 57.8 + - - +
571A GLU* 3.0 24.5 - - + +
573A ILE* 2.8 40.7 + - + +
575A VAL* 4.1 9.0 - - + -
756A SER* 5.3 2.2 - - - +
759A ILE* 4.8 8.7 - - + -
760A LYS* 6.5 0.4 - - + -
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Residues in contact with ALA 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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510A PRO* 4.0 8.1 - - + -
529A ILE* 3.9 26.9 - - + +
531A PRO* 3.3 19.2 - - - +
564A ALA 3.2 13.7 + - - +
565A THR 4.0 1.1 - - - +
566A TYR 3.2 0.2 - - - -
567A LEU* 1.3 78.3 - - - +
569A SER* 1.3 66.8 + - - +
572A ASN* 3.1 19.2 + - - -
573A ILE 3.1 22.6 + - - +
575A VAL* 5.0 0.4 - - + -
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Residues in contact with SER 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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42A THR* 3.1 15.1 - - - +
43A TYR* 2.7 42.1 + - - +
508A GLN 3.1 12.9 + - - -
510A PRO* 3.9 13.6 - - - +
532A PRO* 3.6 16.3 - - - +
565A THR 2.8 19.7 + - - -
568A ALA* 1.3 80.5 - - - +
570A THR* 1.3 59.6 + - - +
572A ASN* 3.8 9.7 + - - -
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Residues in contact with THR 570 (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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42A THR* 2.7 21.9 + - + +
43A TYR 2.5 25.8 + - - -
44A THR* 3.4 8.6 - - + -
566A TYR* 2.7 30.9 + - + -
569A SER* 1.3 74.9 - - - +
571A GLU* 1.3 77.0 + - - +
572A ASN* 3.4 7.0 + - - +
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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