Contacts of the helix formed by residues 1050 - 1055 (chain A) in PDB entry 3GJN
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 SER1050 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037A ILE* 3.5 31.9 - - - +
1040A PHE* 4.9 0.2 - - - -
1041A GLU* 3.2 9.1 + - - -
1048A SER 3.0 0.6 + - - -
1049A GLY* 1.3 66.9 - - - -
1051A ASP* 1.3 66.6 + - - +
1052A LEU 3.0 1.3 - - - -
1053A ILE* 2.8 22.2 + - - +
1054A TYR* 3.1 28.3 + - - -
528B LYS* 6.0 1.6 - - - +
529B THR 5.2 3.5 + - - -
531B THR* 3.1 19.2 + - - +
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Residues in contact with ASP1051 (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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1048A SER* 2.9 26.5 + - - +
1050A SER* 1.3 78.1 + - - +
1052A LEU* 1.3 60.9 + - - +
1055A TRP* 2.8 52.3 + - + +
529B THR 4.3 0.9 - - - +
530B ARG* 3.3 23.6 + - - +
531B THR* 3.0 34.5 + - - +
532B GLN* 5.2 3.8 - - - +
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Residues in contact with LEU1052 (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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1040A PHE* 4.1 15.5 - - + -
1046A HIS* 3.9 28.5 - - + +
1048A SER* 3.7 23.5 + - - +
1049A GLY 3.2 16.0 + - - +
1050A SER 3.0 0.8 - - - -
1051A ASP* 1.3 78.8 - - - +
1053A ILE* 1.3 58.9 + - - +
1056A PRO* 4.3 14.7 - - - +
1060A ASP* 5.6 5.6 - - - +
1062A ASP* 5.0 1.0 - - - +
1067A ILE* 3.9 25.5 - - + +
1070A THR* 4.6 12.3 - - - +
1071A VAL* 3.7 29.8 - - + -
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Residues in contact with ILE1053 (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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1019A VAL* 5.2 1.8 - - + -
1022A ILE* 4.0 20.6 - - + -
1023A CYS* 3.8 26.5 - - + -
1037A ILE* 4.9 2.9 - - + -
1040A PHE* 3.6 46.4 - - + -
1050A SER* 2.8 22.2 + - - +
1052A LEU* 1.3 81.5 - - - +
1054A TYR* 1.3 83.0 + - + +
1056A PRO* 4.2 7.6 - - - +
1062A ASP* 4.8 1.6 - - - +
1067A ILE* 4.3 15.7 - - + -
514B SER* 4.1 2.1 + - - -
516B ASN* 3.1 26.6 - - - +
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Residues in contact with TYR1054 (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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1022A ILE* 4.1 10.2 + - + +
1023A CYS* 6.1 1.3 - - - -
1033A LEU* 3.5 30.0 - - - +
1037A ILE* 3.6 17.5 - - + +
1050A SER* 3.1 27.7 + - - +
1053A ILE* 1.3 90.4 - - + +
1055A TRP* 1.4 76.2 + - + +
1056A PRO* 3.4 4.5 - - - -
514B SER* 2.6 28.4 + - - -
516B ASN* 4.0 24.0 - - + -
517B ASN* 3.4 31.0 + - - +
520B ARG* 3.8 19.2 - - + +
528B LYS* 3.6 27.4 - - + -
529B THR 5.4 0.7 - - - +
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Residues in contact with TRP1055 (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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1050A SER 6.0 0.2 - - - -
1051A ASP* 2.8 35.6 + - - +
1054A TYR* 1.4 82.6 - - + +
1056A PRO* 1.4 64.5 - - + +
1057A LYS* 3.9 1.0 + - - +
465B LEU* 5.8 4.5 - - + -
512B GLN 4.0 22.7 - - - -
513B PHE* 4.3 18.4 - + - -
514B SER* 5.6 1.3 - - - -
517B ASN* 3.6 17.4 - - - +
528B LYS 2.8 24.7 + - - -
529B THR 3.8 6.5 - - - -
530B ARG* 3.4 73.1 + - + +
541B PHE* 4.1 20.0 - + - -
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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