Contacts of the helix formed by residues 941 - 949 (chain A) in PDB entry 1N35
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 LYS 941 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ASN* 3.5 24.2 - - - +
28A GLU* 4.5 2.0 - - - +
866A PRO* 3.6 8.6 - - + +
868A TRP* 3.5 6.8 - - - -
937A PHE 3.4 0.8 + - - -
938A ASN 3.4 9.9 + - - +
939A GLU* 3.1 10.2 - - - +
940A LEU* 1.3 80.7 - - - +
942A LEU* 1.3 56.1 + - - +
943A TYR 3.3 2.2 - - - -
944A GLN* 3.1 29.1 - - + +
945A GLY* 2.8 29.3 + - - -
1042A ARG* 3.3 50.2 + - - +
1043A ARG* 5.4 1.4 + - - +
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Residues in contact with LEU 942 (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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868A TRP* 3.4 40.5 - - + +
881A PHE* 4.7 5.6 - - + -
899A MET* 4.6 6.0 - - + +
902A TRP* 4.1 26.7 - - + -
903A ILE* 5.4 0.4 - - + -
910A MET* 5.0 0.4 - - + -
937A PHE* 3.0 44.0 + - + +
940A LEU* 3.2 5.5 - - + -
941A LYS* 1.3 75.5 - - - +
943A TYR* 1.3 64.0 - - + +
946A TYR* 3.0 27.9 + - - +
1049A PHE* 3.4 38.4 - - + -
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Residues in contact with TYR 943 (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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933A TYR* 3.6 24.3 - - - -
934A ARG* 4.0 11.4 - - - -
937A PHE* 3.1 35.9 + + + -
938A ASN* 3.7 11.4 - - - -
942A LEU* 1.3 73.6 - - - +
944A GLN* 1.3 74.0 + - - +
946A TYR* 3.0 5.3 + - - +
947A TYR* 2.9 30.9 + + + -
1046A TYR* 3.5 49.4 - - + -
1047A SER 3.6 4.4 - - - -
1048A SER* 3.5 41.1 + - - -
1049A PHE* 3.9 30.0 - + - -
1054A GLU* 4.8 1.4 + - - -
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Residues in contact with GLN 944 (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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937A PHE 3.4 7.1 - - - +
938A ASN* 2.9 40.3 + - - +
941A LYS* 3.1 38.1 - - + +
943A TYR* 1.3 74.8 - - - +
945A GLY* 1.3 58.3 + - - +
947A TYR* 3.2 1.6 + - - +
948A MET* 2.8 51.5 + - + +
1041A ALA 4.2 4.0 - - - +
1042A ARG* 3.5 23.1 - - - +
1044A HIS 3.1 19.6 + - - +
1045A SER* 3.8 0.4 - - - +
1046A TYR* 3.5 17.7 - - - -
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Residues in contact with GLY 945 (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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866A PRO* 3.5 19.4 - - - +
868A TRP* 4.4 0.9 - - - -
869A SER* 2.6 39.0 + - - -
941A LYS 2.8 17.8 + - - -
942A LEU 4.2 0.4 - - - -
944A GLN* 1.3 73.3 - - - +
946A TYR* 1.3 62.6 + - - +
948A MET* 4.1 0.4 - - - -
949A ALA* 3.0 16.6 + - - +
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Residues in contact with TYR 946 (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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868A TRP* 4.6 6.1 - - - +
872A TYR* 3.6 27.7 - + - -
896A ASP* 2.6 29.6 + - - -
899A MET* 3.9 16.2 - - + -
942A LEU 3.0 21.4 + - - +
943A TYR* 3.1 5.6 - - - +
945A GLY* 1.3 78.3 - - - +
947A TYR* 1.3 98.6 + + - +
949A ALA* 3.8 6.3 - - - +
950A GLN* 2.9 40.8 + - - +
1049A PHE* 3.8 28.0 - + + -
1050A SER* 3.1 26.5 + - - -
1053A LEU* 3.9 7.2 - - + +
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Residues in contact with TYR 947 (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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943A TYR* 2.9 28.9 + + + +
944A GLN 3.9 2.2 - - - +
946A TYR* 1.3 98.9 - + - +
948A MET* 1.3 65.9 + - - +
949A ALA 3.2 1.8 - - - -
950A GLN* 3.1 25.7 + - + +
951A LEU* 3.5 16.2 - - - +
1041A ALA* 5.1 2.0 - - + -
1046A TYR* 3.4 57.0 - + + +
1048A SER* 2.6 28.0 + - - -
1049A PHE 3.1 18.9 + - - -
1050A SER* 4.4 4.4 - - - -
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Residues in contact with MET 948 (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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863A LEU* 6.4 1.6 - - - -
864A GLN 4.0 9.6 - - - +
865A TYR* 3.7 18.8 + - + -
866A PRO* 3.4 26.5 - - + -
869A SER* 4.0 5.8 - - - +
873A TRP* 4.9 0.2 - - - -
944A GLN* 2.8 53.8 + - + +
945A GLY 3.9 3.1 - - - +
947A TYR* 1.3 72.3 - - - +
949A ALA* 1.3 62.8 + - - +
951A LEU* 3.1 26.5 + - - +
1038A LEU* 3.7 29.6 - - + +
1041A ALA* 4.0 10.5 - - + -
1042A ARG* 3.5 31.9 - - + -
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Residues in contact with ALA 949 (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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869A SER* 3.8 12.5 + - - +
872A TYR* 3.4 30.1 - - + -
873A TRP* 3.1 28.0 + - + +
945A GLY 3.0 17.2 + - - +
946A TYR 3.8 3.1 - - - +
947A TYR 3.2 0.4 - - - -
948A MET* 1.3 77.6 - - - +
950A GLN* 1.3 57.0 + - - +
951A LEU 3.3 1.6 + - - -
953A ARG* 2.8 31.2 + - - -
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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