Contacts of the helix formed by residues 4101 - 4106 (chain D) in PDB entry 1HKN
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 LYS4101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4069D THR* 4.9 8.7 - - - -
4081D GLU* 3.1 53.1 + - + +
4082D GLU* 3.8 31.9 - - + -
4099D SER* 3.3 3.0 + - - +
4100D LYS* 1.3 79.5 - - - +
4102D HIS* 1.3 87.0 + - + +
4103D ALA 3.6 0.4 - - - -
4104D GLU* 3.8 8.2 - - - +
4105D LYS* 4.2 3.3 + - - -
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Residues in contact with HIS4102 (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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4067D MET* 4.2 8.9 + - - -
4068D ASP 4.2 12.3 - - - -
4069D THR* 3.7 21.8 - - - +
4099D SER* 3.1 23.2 + - - +
4100D LYS 3.0 0.4 - - - -
4101D LYS* 1.3 115.3 - - + +
4103D ALA* 1.3 62.4 + - - +
4104D GLU* 3.0 11.7 - - - -
4105D LYS* 3.1 41.1 + - + +
4106D ASN 3.4 6.4 + - - -
4107D TRP* 3.4 43.5 + + + -
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Residues in contact with ALA4103 (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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4086D LEU* 3.8 26.5 - - + -
4098D ILE* 3.7 9.7 - - + +
4099D SER 2.7 14.2 + - - +
4100D LYS 3.1 14.2 + - - +
4102D HIS* 1.3 74.8 - - - +
4104D GLU* 1.3 60.9 + - - +
4106D ASN* 2.9 26.5 + - - +
6051F VAL* 4.3 13.5 - - + -
6052F GLY* 4.9 3.4 - - - +
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Residues in contact with GLU4104 (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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1125A TYR* 2.9 39.1 - - + -
1126A GLY* 5.0 6.1 - - - -
4100D LYS 4.6 0.7 - - - +
4101D LYS 3.8 6.2 - - - +
4102D HIS* 3.0 5.2 - - - -
4103D ALA* 1.3 88.3 + - - +
4105D LYS* 1.3 88.4 + - + +
4106D ASN* 3.1 12.2 + - - -
6051F VAL* 5.7 3.2 - - - +
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Residues in contact with LYS4105 (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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1106A ASN* 5.4 4.9 + - - -
1124A HIS* 4.1 16.1 - - + +
1125A TYR* 3.7 30.1 + - + +
1126A GLY* 5.1 3.6 - - - -
4101D LYS 4.2 2.0 + - - -
4102D HIS* 3.1 38.6 + - + +
4104D GLU* 1.3 101.7 + - + +
4106D ASN* 1.3 72.0 + - - +
4107D TRP* 3.6 45.6 - - + +
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Residues in contact with ASN4106 (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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1106A ASN* 5.6 7.0 + - - +
1125A TYR* 5.3 4.4 - - - +
4098D ILE* 4.3 17.1 - - - +
4102D HIS 3.4 0.4 + - - -
4103D ALA 2.9 18.7 + - - +
4104D GLU 3.5 16.4 + - - -
4105D LYS* 1.3 81.1 + - - +
4107D TRP* 1.3 60.6 - - - +
4108D PHE* 3.0 32.8 + - + -
4123D THR* 3.6 7.8 + - - +
4124D HIS* 6.3 0.7 - - - -
6088F ARG* 6.0 0.2 - - - -
6089F LEU* 3.6 41.6 + - + +
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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