Contacts of the helix formed by residues 3142 - 3149 (chain D) in PDB entry 1KY5
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 HIS3142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3114D GLU* 3.1 29.7 + - - -
3117D LEU* 3.8 19.1 - - + +
3118D HIS* 5.9 2.4 + - - -
3137D LEU* 3.1 35.0 - - + +
3138D ILE* 2.8 28.9 + - - +
3141D LYS* 1.3 84.0 + - + +
3143D PRO* 1.3 57.5 - - - +
3144D GLN* 2.6 26.0 + - - +
3145D LEU* 3.3 21.9 + - + +
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Residues in contact with PRO3143 (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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3138D ILE 3.4 1.1 - - - +
3139D HIS 4.0 15.3 - - - +
3140D THR 4.4 8.1 - - - +
3141D LYS 3.3 8.3 - - - +
3142D HIS* 1.3 84.1 - - - +
3144D GLN* 1.3 68.5 + - + +
3145D LEU 3.0 6.3 + - - -
3146D LEU* 3.0 41.4 + - + +
3147D SER 4.6 0.5 + - - -
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Residues in contact with GLN3144 (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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3141D LYS 5.0 0.9 + - - -
3142D HIS* 2.6 39.8 + - - +
3143D PRO* 1.3 77.0 - - + +
3145D LEU* 1.3 69.7 + - + +
3146D LEU 3.5 0.2 - - - -
3147D SER* 3.5 15.7 + - - -
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Residues in contact with LEU3145 (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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3117D LEU* 4.6 13.7 - - + +
3118D HIS* 4.2 23.3 - - + -
3123D PRO* 4.1 23.6 - - + -
3124D LEU* 3.9 27.2 - - + +
3138D ILE* 4.1 10.1 - - + -
3142D HIS* 3.7 29.2 - - + +
3143D PRO 3.0 1.2 - - - -
3144D GLN* 1.3 91.7 - - + +
3146D LEU* 1.3 65.5 + - - +
3147D SER 3.0 3.1 - - - -
3148D GLY* 2.9 16.4 + - - +
3149D ILE* 3.5 14.1 + - + +
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Residues in contact with LEU3146 (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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3127D ILE* 6.3 0.2 - - + -
3138D ILE* 3.3 25.1 - - + -
3139D HIS* 3.4 38.1 - - + +
3143D PRO* 3.0 42.7 + - + +
3145D LEU* 1.3 77.7 - - - +
3147D SER* 1.3 60.4 + - - +
3149D ILE* 3.4 24.6 + - + +
3173D LYS* 3.9 38.4 - - + +
3174D VAL* 4.0 13.7 - - + +
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Residues in contact with SER3147 (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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3143D PRO 4.6 0.8 + - - -
3144D GLN 3.5 16.2 + - - -
3146D LEU* 1.3 79.9 - - - +
3148D GLY* 1.3 61.2 + - - +
3149D ILE 3.5 3.3 + - - +
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Residues in contact with GLY3148 (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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3123D PRO* 6.4 2.0 - - - -
3124D LEU 3.3 6.8 - - - +
3125D ASN* 2.9 26.9 - - - +
3145D LEU* 2.9 9.1 + - - +
3147D SER* 1.3 81.0 + - - +
3149D ILE* 1.3 62.3 + - - +
3150D ARG* 3.8 0.7 + - - +
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Residues in contact with ILE3149 (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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3124D LEU* 3.7 40.6 - - + +
3125D ASN* 3.5 9.2 - - - +
3126D MET* 4.2 2.7 - - - +
3127D ILE* 3.8 20.0 - - + -
3138D ILE* 4.2 17.9 - - + -
3145D LEU 3.5 15.9 - - - +
3146D LEU* 3.4 19.1 + - + +
3147D SER 3.3 4.5 - - - +
3148D GLY* 1.3 79.2 - - - +
3150D ARG* 1.3 63.4 + - - +
3151D GLY 3.4 24.9 - - - +
3174D VAL* 4.0 21.0 - - + +
3175D PRO* 5.0 1.2 - - - +
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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