Contacts of the helix formed by residues 679 - 686 (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 679 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596B ARG* 3.1 48.9 + - - +
597B ARG* 4.0 12.3 - - - +
671B MET* 3.0 33.3 - - - +
673B LEU 3.1 6.8 + - - +
678B ASP* 1.3 81.1 + - - +
680B LEU* 1.3 64.5 + - - +
681B ASP* 3.4 4.2 + - - +
682B HIS* 3.7 20.0 - - - +
683B TYR* 3.1 17.7 + - + -
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Residues in contact with LEU 680 (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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660B GLU* 4.1 5.4 - - - +
673B LEU 3.8 1.0 + - - -
674B PRO* 3.2 25.1 - - + +
675B THR 3.0 22.0 + - - +
676B PRO* 3.5 30.5 + - + +
678B ASP 3.6 1.4 + - - -
679B ASN* 1.3 76.0 - - - +
681B ASP* 1.3 68.1 + - - +
683B TYR* 2.9 23.1 + - + +
684B ARG* 3.2 48.9 + - + +
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Residues in contact with ASP 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B ARG* 6.0 0.7 - - - +
676B PRO* 5.0 8.8 + - - +
678B ASP 5.4 0.8 + - - +
679B ASN* 3.4 2.0 - - - +
680B LEU* 1.3 81.0 - - - +
682B HIS* 1.3 57.4 - - - +
684B ARG* 3.5 6.4 + - - +
685B ASN* 3.1 30.1 + - - +
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Residues in contact with HIS 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B ARG 3.5 13.2 - - - -
597B ARG* 3.1 38.0 + - - +
598B LEU 2.6 23.4 + - - -
599B GLY 4.8 0.9 - - - -
600B THR* 3.5 25.4 - - + -
671B MET* 3.4 28.7 - - + -
679B ASN* 3.4 17.0 + - - +
680B LEU 3.2 0.8 - - - -
681B ASP* 1.3 74.8 - - - +
683B TYR* 1.3 57.8 + - - +
684B ARG 3.0 2.9 - - - -
685B ASN* 4.0 13.2 - - + +
686B SER* 2.6 49.0 + - - -
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Residues in contact with TYR 683 (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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259B ALA* 3.7 20.1 - - + +
658B ARG* 4.9 0.3 - - - +
659B TRP* 3.7 23.9 + - + -
660B GLU* 3.8 25.4 - - + +
667B THR* 3.7 19.8 - - + +
668B GLU* 3.9 3.6 - - - +
671B MET* 3.5 36.8 - - + +
672B GLY 2.6 28.0 + - - -
673B LEU 3.7 1.3 - - - -
674B PRO* 3.4 42.3 - - + +
679B ASN 3.1 22.0 + - - -
680B LEU* 2.9 13.9 + - + +
682B HIS* 1.3 78.3 - - - +
684B ARG* 1.3 59.2 + - - +
686B SER* 3.6 7.3 + - - -
687B THR* 3.7 13.3 - - - +
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Residues in contact with ARG 684 (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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245A SER* 5.9 3.9 + - - +
658B ARG* 3.5 26.6 - - - +
660B GLU* 2.8 37.7 + - - -
680B LEU* 3.2 36.7 + - + +
681B ASP* 3.8 8.3 - - - +
682B HIS 3.0 0.4 - - - -
683B TYR* 1.3 75.8 - - - +
685B ASN* 1.3 59.1 + - - +
686B SER 3.1 6.0 + - - -
687B THR* 3.5 20.2 + - - +
690B SER* 4.6 6.6 - - - -
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Residues in contact with ASN 685 (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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681B ASP* 3.1 19.1 + - - +
682B HIS* 3.1 18.9 + - + +
684B ARG* 1.3 76.2 - - - +
686B SER* 1.3 57.4 + - - +
687B THR 3.7 1.5 + - - -
690B SER* 4.5 8.8 + - - -
691B ARG* 4.6 10.7 + - - -
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Residues in contact with SER 686 (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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598B LEU 3.6 22.9 - - - -
599B GLY* 4.8 1.1 - - - -
634B TYR* 3.0 27.4 + - - -
638B MET* 3.9 10.9 - - - +
657B SER 4.0 0.7 - - - +
658B ARG* 5.0 0.2 - - - -
659B TRP* 3.8 17.1 - - - -
671B MET* 3.9 3.3 - - - +
682B HIS* 2.6 29.7 + - - -
683B TYR 3.6 7.7 + - - -
684B ARG 3.1 0.6 - - - -
685B ASN* 1.3 79.5 - - - +
687B THR* 1.3 63.5 + - - +
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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