Contacts of the helix formed by residues 1050 - 1055 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528C LYS* 5.9 1.6 - - - +
529C THR 5.3 2.9 + - - -
531C THR* 3.6 16.0 + - - +
1037D ILE* 3.5 31.6 - - - +
1040D PHE* 4.7 0.9 - - - -
1041D GLU* 3.2 9.1 + - - -
1048D SER 3.0 1.0 + - - -
1049D GLY* 1.3 70.3 - - - -
1051D ASP* 1.3 70.1 + - - +
1052D LEU 3.0 0.7 - - - -
1053D ILE* 2.7 24.5 + - - +
1054D TYR* 3.0 28.3 + - - -
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Residues in contact with ASP1051 (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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529C THR 4.4 1.6 + - - +
530C ARG* 3.4 27.9 + - - +
531C THR* 2.8 31.2 + - - +
532C GLN* 5.1 4.5 - - - +
1048D SER* 3.0 25.7 + - - +
1050D SER* 1.3 77.2 + - - +
1052D LEU* 1.3 63.1 + - - +
1053D ILE 2.7 0.2 + - - -
1055D TRP* 2.7 50.1 + - - +
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Residues in contact with LEU1052 (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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1040D PHE* 4.5 8.1 - - + -
1046D HIS* 3.7 43.7 - - + +
1048D SER* 3.5 27.1 - - - +
1049D GLY 3.4 13.5 + - - +
1050D SER 3.0 1.2 - - - -
1051D ASP* 1.3 78.9 - - - +
1053D ILE* 1.3 60.0 + - + +
1055D TRP 5.1 1.3 - - - -
1056D PRO* 4.1 16.3 - - - +
1060D ASP* 5.8 4.0 - - - +
1062D ASP* 5.1 1.2 - - - +
1067D ILE* 4.1 20.9 - - + +
1070D THR* 5.4 11.0 - - - +
1071D VAL* 4.0 21.5 - - + -
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Residues in contact with ILE1053 (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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514C SER* 4.3 1.4 + - - -
516C ASN* 3.2 27.0 - - - +
1019D VAL* 5.2 1.3 - - + -
1022D ILE* 3.8 23.6 - - + -
1023D CYS* 3.9 25.6 - - - -
1037D ILE* 5.4 2.2 - - + -
1040D PHE* 3.7 44.2 - - + -
1050D SER* 2.7 15.7 + - - +
1051D ASP 2.7 0.6 + - - -
1052D LEU* 1.3 82.2 - - - +
1054D TYR* 1.4 84.5 + - + +
1056D PRO* 4.1 8.9 - - - +
1062D ASP* 4.8 2.8 - - - +
1067D ILE* 4.4 15.9 - - + -
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Residues in contact with TYR1054 (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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514C SER* 2.6 27.7 + - - -
516C ASN* 4.1 11.4 - - + -
517C ASN* 3.4 41.1 + - - +
520C ARG* 3.8 19.0 - - + +
528C LYS* 3.7 28.5 - - + -
529C THR 5.5 1.1 - - - +
1022D ILE* 3.9 11.6 + - - +
1023D CYS* 6.3 0.7 - - - -
1033D LEU* 3.8 19.2 - - - +
1037D ILE* 3.8 24.7 - - + +
1050D SER* 3.0 26.7 + - - +
1053D ILE* 1.4 96.6 - - + +
1055D TRP* 1.3 76.5 + - + +
1056D PRO* 3.6 2.0 - - - -
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Residues in contact with TRP1055 (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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465C LEU* 5.6 5.2 - - + -
512C GLN 3.8 22.7 - - - -
513C PHE* 4.1 18.6 - + - -
514C SER* 5.4 2.5 - - - -
517C ASN* 3.7 15.6 - - - +
528C LYS 2.8 25.0 + - - -
529C THR 3.9 2.0 - - - -
530C ARG* 3.4 73.0 + - + +
541C PHE* 4.1 20.6 - + - -
1051D ASP* 2.7 35.9 + - + +
1052D LEU* 5.1 0.2 - - - -
1054D TYR* 1.3 79.3 - - + +
1056D PRO* 1.3 65.2 - - - +
1057D LYS 3.8 0.7 + - - -
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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