Contacts of the helix formed by residues 1018 - 1026 (chain D) in PDB entry 6M6C
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 ASN1018 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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953D ASP* 2.7 39.2 + - - +
955D VAL* 4.0 13.5 - - - +
1011D PHE* 4.4 11.5 - - + -
1015D TYR* 3.2 31.0 + - + +
1016D PRO 3.5 0.2 - - - -
1017D PHE* 1.3 78.1 - - - +
1019D PRO* 1.3 75.5 - - - +
1020D LEU* 2.9 28.2 + - - +
1021D TYR* 3.3 13.2 + - + +
1022D VAL* 3.0 20.3 + - - +
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Residues in contact with PRO1019 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971C LYS* 5.4 0.7 - - - +
947D ILE* 4.8 15.2 - - + +
948D THR* 3.2 34.3 - - + +
949D ILE* 4.5 3.1 - - + -
953D ASP* 3.6 27.1 - - + +
1017D PHE 3.4 5.8 - - - +
1018D ASN* 1.3 93.6 - - - +
1020D LEU* 1.3 57.1 + - - +
1022D VAL* 3.4 5.3 + - + +
1023D MET* 2.9 46.5 + - + +
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Residues in contact with LEU1020 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876C VAL* 5.6 1.1 - - + -
877C PRO* 3.7 23.3 - - + -
949D ILE* 4.4 12.3 - - + -
953D ASP* 4.4 17.5 - - + +
954D ALA* 4.4 16.8 - - + +
1011D PHE* 4.8 7.0 - - + -
1018D ASN* 2.9 10.7 + - - +
1019D PRO* 1.3 78.5 - - + +
1021D TYR* 1.3 57.3 + - - +
1023D MET* 3.3 23.2 + - + +
1024D ALA* 2.9 30.4 + - - +
1035D ILE* 4.3 18.9 - - + +
1038D LEU* 3.8 27.8 - - + -
1039D CYS* 4.8 6.5 - - - -
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Residues in contact with TYR1021 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790D TYR* 5.2 5.2 - - - -
1008D PHE* 4.5 16.6 - + + -
1011D PHE* 3.6 41.8 - + + -
1012D GLU* 3.2 37.7 + - + +
1015D TYR 4.3 5.6 - - - -
1016D PRO* 3.8 25.1 - - + -
1018D ASN* 3.3 16.5 + - + +
1020D LEU* 1.3 78.6 - - - +
1022D VAL* 1.3 59.2 + - + +
1024D ALA* 3.3 5.8 + - + +
1025D GLN* 2.9 75.8 + - + +
1035D ILE* 6.1 0.4 - - - -
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Residues in contact with VAL1022 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787D LEU* 3.7 23.6 - - + -
790D TYR* 3.6 35.4 - - + +
791D TYR* 4.9 11.7 - - + -
947D ILE* 5.4 2.9 - - + -
1016D PRO 3.9 20.2 - - - +
1017D PHE* 3.9 19.5 - - + +
1018D ASN 3.0 20.3 + - - +
1019D PRO* 3.8 6.1 - - + +
1021D TYR* 1.3 77.2 - - + +
1023D MET* 1.3 58.8 + - - +
1025D GLN* 4.7 1.8 - - - -
1026D SER* 2.9 31.2 + - - -
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Residues in contact with MET1023 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873C PRO* 4.5 3.1 - - - +
874C LEU* 3.4 38.8 - - + -
877C PRO* 3.6 20.9 - - + -
787D LEU* 4.5 13.5 - - + -
947D ILE* 5.5 4.9 - - + -
949D ILE* 3.6 21.8 - - + -
1019D PRO* 2.9 39.9 + - + +
1020D LEU* 3.3 27.3 + - + +
1022D VAL* 1.3 77.3 - - - +
1024D ALA* 1.3 60.4 + - - +
1026D SER* 4.3 4.3 - - - -
1027D GLY 3.7 0.3 + - - -
1028D ALA* 3.4 10.9 + - + -
1029D ARG 2.8 33.7 + - - +
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Residues in contact with ALA1024 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008D PHE* 5.8 6.3 - - + -
1020D LEU 2.9 17.3 + - - +
1021D TYR* 3.8 8.1 - - + +
1023D MET* 1.3 77.0 - - - +
1025D GLN* 1.3 72.3 + - - +
1027D GLY* 3.3 11.6 + - - -
1029D ARG 3.8 8.0 + - - +
1030D GLY 4.3 10.2 - - - +
1031D ASN* 5.4 3.6 - - - -
1032D PRO* 5.6 3.4 - - + -
1035D ILE* 4.3 20.9 - - + -
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Residues in contact with GLN1025 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790D TYR* 4.0 20.4 - - + +
907D GLU* 4.3 9.9 - - - +
1021D TYR* 2.9 63.2 + - + +
1022D VAL* 4.1 1.8 - - - +
1024D ALA* 1.3 83.4 - - - +
1026D SER* 1.3 62.8 + - - +
1027D GLY* 3.1 1.6 + - - -
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Residues in contact with SER1026 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786D ILE* 3.2 22.9 - - - +
787D LEU* 4.5 5.3 - - - +
790D TYR* 3.7 35.2 - - - -
907D GLU* 3.6 11.2 - - - +
908D LYS* 3.5 12.8 + - - +
1022D VAL* 2.9 20.2 + - - -
1023D MET* 4.0 0.9 + - - -
1025D GLN* 1.3 76.1 - - - +
1027D GLY* 1.3 59.5 + - - +
1028D ALA* 3.3 23.6 + - - +
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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