Contacts of the helix formed by residues 1018 - 1027 (chain N) in PDB entry 4G7Z
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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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950M LEU* 4.8 1.7 - - - +
953N ASP* 3.1 31.1 + - - +
955N VAL* 4.1 5.9 - - - +
1011N PHE* 3.3 29.9 - - + -
1015N TYR* 3.1 28.6 + - + +
1016N PRO 3.4 0.4 - - - -
1017N PHE* 1.3 74.9 - - - +
1019N PRO* 1.3 64.9 - - - +
1020N LEU* 3.1 19.1 + - - +
1021N TYR* 2.9 32.8 + - + +
1022N VAL* 2.9 15.4 + - - +
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Residues in contact with PRO1019 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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950M LEU* 5.6 3.4 - - + -
952M LEU* 6.6 0.4 - - + -
971M LYS* 5.3 1.8 - - - +
946N GLY 5.9 0.2 - - - +
947N ILE* 4.2 19.1 - - + -
948N THR* 3.3 33.9 - - + +
949N ILE* 4.7 2.2 - - + -
953N ASP* 3.3 19.3 - - - +
1017N PHE 3.3 7.8 - - - +
1018N ASN* 1.3 95.9 - - - +
1020N LEU* 1.3 65.9 + - + +
1022N VAL* 3.4 7.3 + - + +
1023N MET* 3.0 33.8 + - + +
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Residues in contact with LEU1020 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877M PRO* 5.1 4.9 - - + -
949N ILE* 3.7 32.8 - - + -
953N ASP* 3.3 28.3 - - + +
954N ALA* 3.9 15.5 - - + -
1011N PHE* 4.7 4.7 - - + -
1018N ASN* 3.1 9.2 + - - +
1019N PRO* 1.3 78.6 - - - +
1021N TYR* 1.3 58.1 + - - +
1023N MET* 3.8 13.2 - - + +
1024N ALA* 3.0 32.0 + - - +
1035N ILE* 4.1 24.9 - - + +
1038N LEU* 4.2 22.4 - - + -
1039N CYS* 4.3 11.0 - - - -
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Residues in contact with TYR1021 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790N TYR* 5.2 5.4 - - - -
1008N PHE* 3.9 40.2 - + - -
1011N PHE* 3.5 29.3 - + + -
1012N GLU* 3.7 30.4 - - - +
1015N TYR 4.6 0.2 - - - +
1016N PRO* 3.3 30.7 - - + -
1018N ASN* 2.9 19.1 + - + +
1020N LEU* 1.3 78.1 - - - +
1022N VAL* 1.3 59.0 + - - +
1024N ALA* 3.8 3.0 - - - +
1025N GLN* 2.9 66.6 + - + +
1035N ILE* 6.3 0.7 - - - -
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Residues in contact with VAL1022 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787N LEU* 3.7 23.1 - - + +
790N TYR* 3.7 33.1 - - + -
791N TYR* 5.6 4.3 - - + +
947N ILE* 5.1 11.9 - - + -
1016N PRO 4.3 4.3 - - - +
1017N PHE* 3.5 35.9 - - + +
1018N ASN 2.9 20.3 + - - +
1019N PRO* 3.6 9.2 - - + +
1020N LEU 3.3 0.2 - - - -
1021N TYR* 1.3 77.6 - - - +
1023N MET* 1.3 52.9 + - - +
1025N GLN* 3.9 1.4 - - - +
1026N SER* 2.6 40.4 + - - -
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Residues in contact with MET1023 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873M PRO* 4.7 0.4 - - - -
874M LEU* 3.4 38.1 - - + -
877M PRO* 3.6 32.3 - - + -
787N LEU* 4.0 13.2 - - + -
947N ILE* 4.9 8.3 - - + -
949N ILE* 3.7 24.0 - - + -
1019N PRO* 3.0 22.3 + - + +
1020N LEU* 3.8 16.4 - - + +
1022N VAL* 1.3 78.7 - - - +
1024N ALA* 1.3 59.9 + - - +
1026N SER* 3.6 4.9 - - - -
1027N GLY 3.1 17.3 + - - -
1028N ALA* 3.2 6.3 + - - -
1029N ARG* 2.7 29.6 - - + +
1030N GLY* 5.7 0.2 - - - -
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Residues in contact with ALA1024 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008N PHE* 4.6 15.0 - - + -
1020N LEU 3.0 18.9 + - - +
1021N TYR* 3.9 5.2 - - - +
1023N MET* 1.3 78.1 - - - +
1025N GLN* 1.3 63.7 + - - +
1027N GLY* 3.8 6.8 + - - -
1029N ARG 3.2 11.1 + - - +
1030N GLY 4.2 10.9 - - - +
1031N ASN* 4.8 3.2 - - - +
1032N PRO* 5.5 1.9 - - + +
1035N ILE* 4.2 23.1 - - + -
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Residues in contact with GLN1025 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790N TYR* 4.1 18.6 - - + +
907N GLU* 4.2 8.7 - - - +
1008N PHE* 3.9 20.6 - - - -
1021N TYR* 2.9 63.1 + - + +
1022N VAL 3.9 1.6 - - - +
1024N ALA* 1.3 78.7 - - - +
1026N SER* 1.3 63.5 + - - +
1027N GLY* 3.2 0.9 + - - -
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Residues in contact with SER1026 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786N ILE* 3.4 16.7 - - - +
787N LEU* 4.6 1.7 - - - +
790N TYR* 3.5 31.8 - - - -
907N GLU* 3.1 11.2 - - - +
908N LYS* 2.9 30.0 + - - +
1022N VAL* 2.6 26.5 + - - +
1023N MET* 3.3 7.6 + - - -
1025N GLN* 1.3 75.6 - - - +
1027N GLY* 1.3 60.9 + - - +
1028N ALA* 3.4 11.0 + - - +
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Residues in contact with GLY1027 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782N SER 4.2 2.1 - - - +
783N ARG* 4.4 4.2 + - - -
786N ILE* 3.8 13.1 - - - +
908N LYS* 4.4 16.3 - - - +
1023N MET 3.1 7.3 + - - -
1024N ALA 3.8 5.8 + - - -
1025N GLN 3.2 3.4 - - - -
1026N SER* 1.3 79.4 - - - +
1028N ALA* 1.3 65.5 + - - +
1029N ARG* 3.4 4.2 - - - -
1030N GLY 5.7 1.3 - - - -
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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