Contacts of the helix formed by residues 3082 - 3093 (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 SER3082 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3078D SER 3.1 13.1 + - - -
3079D TYR 3.4 1.8 - - - -
3081D LYS* 1.3 84.9 + - - +
3083D ALA* 1.3 63.8 + - - +
3084D SER* 3.3 3.6 - - - -
3085D GLU* 3.0 26.4 + - - +
3086D ILE* 2.9 31.0 + - - +
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Residues in contact with ALA3083 (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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3079D TYR* 2.7 54.3 + - + +
3080D THR* 4.4 6.5 + - - +
3081D LYS 3.8 1.2 - - - -
3082D SER* 1.3 71.5 - - - +
3084D SER* 1.3 64.5 + - - +
3086D ILE* 4.6 0.7 - - - -
3087D ASN* 2.9 33.3 + - - +
3174D SER* 5.4 0.9 - - - +
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Residues in contact with SER3084 (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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42A TYR* 4.0 12.0 + - - -
3082D SER 3.3 1.2 - - - -
3083D ALA* 1.3 77.3 - - - +
3085D GLU* 1.3 57.6 + - - +
3087D ASN* 4.3 2.9 - - - +
3088D GLY* 2.9 26.9 + - - -
3091D ARG* 5.1 1.7 + - - +
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Residues in contact with GLU3085 (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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41A ALA 5.6 2.6 - - - +
42A TYR* 4.0 15.3 - - + -
3082D SER* 3.0 26.6 + - - +
3084D SER* 1.3 78.2 - - - +
3086D ILE* 1.3 62.9 + - + +
3088D GLY* 3.3 0.9 + - - -
3089D LYS* 2.9 50.5 + - + +
3104D LEU* 6.1 1.3 - - + -
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Residues in contact with ILE3086 (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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3079D TYR* 3.8 24.5 - - + -
3082D SER* 2.9 29.1 + - - +
3083D ALA* 3.9 4.0 - - - +
3085D GLU* 1.3 78.9 - - + +
3087D ASN* 1.3 58.5 + - - +
3089D LYS* 3.3 8.0 + - - +
3090D LEU* 3.0 44.3 + - + +
3100D PHE* 5.2 1.0 - - + -
3104D LEU* 4.0 18.2 - - + -
3107D GLN* 3.6 34.8 - - + +
3108D VAL* 4.5 12.8 - - + -
3111D LEU* 6.3 0.2 - - + -
3172D TYR* 4.2 16.6 - - + -
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Residues in contact with ASN3087 (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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3079D TYR* 3.1 25.1 + - - -
3083D ALA* 2.9 25.1 + - - +
3084D SER* 4.3 2.4 - - - +
3086D ILE* 1.3 70.9 - - - +
3088D GLY* 1.3 60.6 + - - +
3090D LEU* 3.3 5.1 + - - +
3091D ARG* 2.9 61.1 + - - +
3171D GLY* 3.4 3.3 - - - -
3172D TYR* 2.8 49.4 + - - -
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Residues in contact with GLY3088 (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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42A TYR* 3.6 27.6 - - - +
3084D SER 2.9 19.5 + - - -
3085D GLU 3.7 1.6 - - - -
3086D ILE 3.2 0.4 - - - -
3087D ASN* 1.3 78.9 - - - +
3089D LYS* 1.3 56.2 + - - +
3091D ARG* 3.3 11.9 + - - +
3092D GLN* 2.9 31.4 + - - +
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Residues in contact with LYS3089 (chain D).
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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41A ALA 5.0 2.6 + - - +
42A TYR* 3.2 38.1 + - + +
43A SER 3.5 12.9 + - - -
44A ASN* 3.0 27.3 + - - +
3085D GLU* 2.9 33.3 + - + +
3086D ILE* 3.8 4.5 - - - +
3088D GLY* 1.3 72.6 - - - +
3090D LEU* 1.3 67.1 + - - +
3093D ASN* 2.9 30.7 + - - +
3100D PHE* 3.6 25.0 - - + -
3101D PRO* 4.3 9.9 - - - +
3104D LEU* 3.8 23.3 - - + -
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Residues in contact with LEU3090 (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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3086D ILE* 3.0 25.2 + - + +
3087D ASN* 3.6 6.5 - - - +
3088D GLY 3.2 0.2 - - - -
3089D LYS* 1.3 77.2 - - - +
3091D ARG* 1.3 57.0 + - - +
3093D ASN* 5.1 0.2 - - - -
3094D LYS* 3.0 9.2 + - - -
3095D GLY* 2.9 32.1 + - - +
3097D ILE* 3.9 7.2 - - + -
3100D PHE* 3.9 22.7 - - + -
3108D VAL* 5.0 3.1 - - + -
3170D TYR* 3.6 25.0 - - - +
3171D GLY* 3.9 6.1 - - - -
3172D TYR* 3.7 36.6 - - + -
3219D ARG* 3.7 31.6 - - - +
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Residues in contact with ARG3091 (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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3084D SER 5.1 1.2 + - - -
3087D ASN* 2.9 58.0 + - - +
3088D GLY* 3.7 9.5 - - - +
3090D LEU* 1.3 77.1 - - - +
3092D GLN* 1.3 62.0 + - - +
3094D LYS* 3.1 16.6 + - - +
3128D ARG* 6.0 1.8 - - - +
3169D GLU* 2.9 37.6 + - - +
3170D TYR* 3.8 23.1 - - + -
3171D GLY 4.4 0.7 - - - +
3172D TYR 5.0 3.4 + - - -
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Residues in contact with GLN3092 (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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41A ALA* 5.0 4.8 - - - +
42A TYR* 3.3 34.1 + - + +
43A SER* 3.2 38.0 - - - +
3088D GLY 2.9 17.2 + - - +
3089D LYS 4.1 2.0 - - - +
3091D ARG* 1.3 77.0 - - - +
3093D ASN* 1.3 60.8 + - - +
3094D LYS* 3.7 4.9 + - - +
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Residues in contact with ASN3093 (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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42A TYR 3.4 21.6 + - - -
43A SER* 5.0 0.9 - - - +
44A ASN* 3.2 27.8 + - - +
3089D LYS 2.9 25.4 + - - +
3090D LEU 4.4 0.4 - - - +
3092D GLN* 1.3 80.8 - - - +
3094D LYS* 1.3 70.9 + - - +
3095D GLY 3.2 1.1 - - - -
3096D VAL* 3.0 37.4 + - + +
3100D PHE* 3.5 13.2 - - + -
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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