Contacts of the helix formed by residues 3051 - 3064 (chain D) in PDB entry 1G24
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 ASN3051 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3049D PHE* 4.9 0.9 - - - -
3050D THR* 1.3 83.4 + - - +
3052D ILE* 1.3 60.2 + - - +
3053D ASP* 3.5 18.5 + - - +
3054D GLN* 2.9 41.5 + - + +
3055D ALA* 2.8 27.0 + - - +
3178D MET* 4.0 2.5 - - - -
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Residues in contact with ILE3052 (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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3050D THR 4.0 0.6 + - - -
3051D ASN* 1.3 72.9 + - - +
3053D ASP* 1.3 62.9 + - - +
3055D ALA* 3.3 2.4 + - - +
3056D LYS* 3.0 45.6 + - + +
3178D MET* 3.5 31.2 - - + -
3180D VAL* 5.7 4.0 - - + -
3212D GLN* 4.8 18.2 - - - +
3213D LEU* 4.3 13.2 - - + -
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Residues in contact with ASP3053 (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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3051D ASN* 3.2 16.5 + - - +
3052D ILE* 1.3 81.6 - - - +
3054D GLN* 1.3 58.3 + - + +
3056D LYS* 3.7 7.3 + - - +
3057D ALA* 3.1 25.5 + - - +
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Residues in contact with GLN3054 (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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3049D PHE* 4.3 7.4 - - + -
3051D ASN* 2.9 35.7 + - + +
3053D ASP* 1.3 78.6 - - + +
3055D ALA* 1.3 56.8 + - - +
3056D LYS 3.2 0.2 - - - -
3057D ALA* 3.6 16.6 - - - +
3058D TRP* 2.7 36.4 + - - +
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Residues in contact with ALA3055 (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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3049D PHE* 3.6 35.4 - - + -
3051D ASN 2.8 12.5 + - - +
3052D ILE* 3.6 12.8 - - - +
3054D GLN* 1.3 76.3 - - - +
3056D LYS* 1.3 57.6 + - - +
3058D TRP* 3.3 0.9 + - - +
3059D GLY* 2.8 26.3 + - - -
3177D LEU* 3.6 21.9 - - + +
3178D MET* 4.3 1.8 - - - -
3202D TYR* 4.3 0.2 + - - -
3213D LEU* 4.2 14.6 - - + -
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Residues in contact with LYS3056 (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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3052D ILE* 3.0 31.8 + - + +
3053D ASP* 3.7 7.9 - - - +
3055D ALA* 1.3 76.0 - - - +
3057D ALA* 1.3 57.5 + - - +
3059D GLY* 3.2 1.2 + - - -
3060D ASN* 2.8 42.7 + - - +
3202D TYR* 3.4 17.0 - - - +
3204D ASP* 2.8 30.4 + - - +
3212D GLN* 4.8 12.3 - - - +
3213D LEU* 3.4 19.4 - - + +
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Residues in contact with ALA3057 (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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3053D ASP 3.1 16.0 + - - +
3054D GLN* 3.3 19.0 + - - +
3056D LYS* 1.3 78.9 - - - +
3058D TRP* 1.3 57.4 + - - +
3060D ASN* 3.8 7.6 - - - +
3061D ALA* 3.0 29.2 + - - +
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Residues in contact with TRP3058 (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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3049D PHE* 3.3 32.7 - + + -
3054D GLN 2.7 21.1 + - - +
3055D ALA 3.6 2.5 - - - +
3057D ALA* 1.3 69.7 - - - +
3059D GLY* 1.3 73.9 + - - +
3061D ALA* 3.2 5.5 + - + -
3062D GLN* 3.0 51.7 + - + +
3120D THR* 3.7 18.8 - - - -
3121D PRO* 3.6 30.0 - - + +
3122D GLU* 4.2 22.4 + - + +
3124D ILE* 4.3 7.6 - - + -
3177D LEU* 4.1 13.9 - - + -
3215D MET* 3.6 28.9 - - + -
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Residues in contact with GLY3059 (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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3055D ALA 2.8 16.1 + - - -
3058D TRP* 1.3 87.2 - - - +
3060D ASN* 1.3 61.7 + - - +
3062D GLN* 3.0 5.9 + - - +
3063D TYR 2.9 19.2 + - - -
3202D TYR* 3.2 40.5 - - - -
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Residues in contact with ASN3060 (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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3056D LYS* 2.8 29.8 + - - +
3057D ALA* 3.8 7.4 - - - +
3059D GLY* 1.3 71.6 - - - +
3061D ALA* 1.3 57.9 + - - +
3063D TYR* 3.3 7.5 + - + +
3064D LYS* 2.9 39.4 + - + +
3202D TYR* 3.4 19.4 + - - -
3204D ASP* 5.4 0.8 + - - -
3205D PRO* 3.9 19.4 - - - +
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Residues in contact with ALA3061 (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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3057D ALA 3.0 17.5 + - - +
3058D TRP* 3.4 8.1 - - - +
3060D ASN* 1.3 78.7 - - - +
3062D GLN* 1.3 71.1 + - - +
3064D LYS* 3.8 9.8 + - - +
3065D LYS* 3.8 21.7 - - - +
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Residues in contact with GLN3062 (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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3058D TRP* 3.0 65.7 + - + +
3059D GLY* 3.0 6.0 + - - +
3061D ALA* 1.3 82.4 - - - +
3063D TYR* 1.3 67.5 + - - +
3065D LYS* 3.0 32.6 + - - +
3066D TYR* 3.2 35.4 + - + +
3119D LYS 5.1 2.8 - - - +
3121D PRO* 3.4 30.8 - - + +
3202D TYR* 5.1 0.9 - - + -
3215D MET* 5.7 0.7 - - + -
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Residues in contact with TYR3063 (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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3059D GLY 2.9 13.4 + - - +
3060D ASN* 3.3 12.8 + - + +
3062D GLN* 1.3 77.2 - - - +
3064D LYS* 1.3 92.9 + - + +
3065D LYS 3.0 1.6 + - - -
3066D TYR* 3.1 39.5 + + + +
3067D GLY 4.5 1.2 + - - -
3068D LEU* 4.4 6.1 - - + -
3073D LYS* 3.0 32.8 - - - +
3202D TYR 4.2 5.2 - - - +
3205D PRO* 3.9 29.0 + - + -
3206D ILE* 3.3 37.8 - - + +
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Residues in contact with LYS3064 (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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3060D ASN* 2.9 24.3 + - + +
3061D ALA* 4.1 7.6 - - - +
3062D GLN 3.3 0.2 - - - -
3063D TYR* 1.3 100.8 - - + +
3065D LYS* 1.3 62.6 + - + +
3066D TYR 3.5 0.4 + - - -
3067D GLY 4.9 2.5 + - - -
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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