Contacts of the strand formed by residues 4085 - 4089 (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 PHE4085 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4053D GLU* 3.4 3.9 - - - -
4054D VAL* 2.9 45.8 + - + +
4056D ILE* 4.7 8.3 - - + -
4065D LEU* 3.5 39.9 - - + -
4066D ALA* 3.9 23.8 - - - -
4067D MET* 4.0 9.0 - - + -
4073D LEU* 4.5 0.4 - - + -
4082D GLU 4.0 2.9 - - - -
4083D CYS 3.4 15.9 - - - -
4084D LEU* 1.3 72.7 - - - +
4086D LEU* 1.3 65.1 + - - +
4087D GLU 3.5 0.5 + - - -
4097D TYR* 4.2 15.0 - - + -
4098D ILE 3.1 18.2 - - - +
4099D SER* 3.6 21.8 - - - -
4100D LYS 4.1 0.4 - - - +
4109D VAL* 3.3 33.4 - - + -
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Residues in contact with LEU4086 (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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4052D GLY 3.4 4.0 - - - +
4053D GLU* 4.1 28.3 - - + +
4085D PHE* 1.3 73.0 - - - +
4087D GLU* 1.3 60.8 + - - +
4088D ARG* 3.4 40.9 - - - +
4097D TYR* 3.4 4.1 - - - -
4098D ILE* 2.7 45.9 + - + +
4100D LYS* 4.2 19.3 - - + -
4103D ALA* 3.8 27.4 - - + -
6051F VAL 4.3 7.2 - - - +
6052F GLY* 3.9 15.7 - - - -
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Residues in contact with GLU4087 (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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4046D LEU* 3.6 11.6 - - - +
4052D GLY* 2.7 25.5 + - - +
4054D VAL* 3.6 22.7 - - + +
4085D PHE 3.5 1.2 + - - -
4086D LEU* 1.3 69.6 - - - +
4088D ARG* 1.3 79.2 + - - +
4089D LEU 4.4 0.6 + - - +
4095D ASN* 3.5 18.3 + - - +
4096D THR 3.6 3.8 - - - -
4097D TYR* 2.7 44.6 + - + -
4134D PRO* 5.2 0.2 - - - +
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Residues in contact with ARG4088 (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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4052D GLY* 4.5 6.6 + - - -
4086D LEU* 3.4 47.4 - - - +
4087D GLU* 1.3 90.9 + - - +
4089D LEU* 1.3 61.7 + - - +
4090D GLU* 3.6 8.9 - - - +
4095D ASN* 3.2 7.0 - - - -
4096D THR* 2.9 47.8 + - - +
4098D ILE* 5.0 13.4 - - + +
6052F GLY* 4.0 10.3 + - - -
6086F LEU* 3.2 51.2 - - - +
6087F GLU 5.3 2.6 + - - -
6088F ARG* 4.0 32.1 - - + +
6098F ILE* 5.9 0.7 - - + -
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Residues in contact with LEU4089 (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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4087D GLU* 4.4 1.0 + - - +
4088D ARG* 1.3 73.9 - - - +
4090D GLU* 1.3 90.5 + - - +
4093D HIS* 3.9 17.0 - - - +
4094D TYR 3.6 7.4 - - - +
4095D ASN* 3.2 17.9 - - - +
6088F ARG* 3.9 2.3 + - - -
6104F GLU* 4.4 20.0 - - - +
6106F ASN* 3.3 19.8 - - - +
6125F TYR* 2.6 27.9 + - - -
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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