Contacts of the helix formed by residues 28 - 33 (chain B) in PDB entry 4K9N
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 GLU 28 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PRO* 5.0 0.9 - - + -
25B GLY* 3.0 28.1 + - - +
27B ASN* 1.3 86.6 - - - +
29B LEU* 1.3 65.0 + - - +
30B PRO* 3.2 3.4 - - - -
31B PHE* 2.9 18.9 + - + +
32B LEU* 3.0 19.3 + - + +
68B ASN* 3.3 28.9 - - - +
69B LEU 3.2 23.9 - - - +
70B HIS* 2.9 29.5 + - - +
71B SER 3.4 0.9 + - - -
97B GLY* 2.8 33.8 + - - +
163B TRP* 5.8 0.2 - - - +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PRO* 5.0 3.8 - - + -
25B GLY 3.3 23.0 + - - +
26B SER* 3.3 6.9 + - - +
28B GLU* 1.3 78.4 - - - +
30B PRO* 1.3 65.3 - - + +
32B LEU* 3.2 3.4 + - + +
33B LYS* 2.9 32.5 + - - +
461D LEU* 4.1 10.8 - - + +
464D PHE* 4.3 11.7 - - + -
465D ALA* 3.5 42.8 - - + +
468D LEU* 3.9 15.5 - - + -
470D ALA* 4.8 2.5 - - + -
473D VAL* 4.2 26.5 - - + +
476D LEU* 4.7 12.8 - - + -
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Residues in contact with PRO 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B HIS* 3.3 8.1 - - - -
26B SER 3.5 9.9 - - - +
27B ASN 4.0 5.2 - - - +
28B GLU 3.4 3.8 - - - -
29B LEU* 1.3 95.7 - - + +
31B PHE* 1.3 58.2 + - - +
33B LYS* 2.7 38.8 + - + +
160B TYR* 3.4 42.8 - - + +
163B TRP* 3.8 9.9 - - + +
164B ASP* 5.3 5.4 - - - +
468D LEU* 4.3 15.0 - - + -
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B HIS* 3.1 19.0 + - - -
8B THR* 4.5 9.0 - - + -
9B TYR* 2.8 57.3 + + - -
12B LEU* 4.5 2.7 - - + -
20B VAL* 4.9 3.6 - - + -
28B GLU* 2.9 12.4 + - - +
30B PRO* 1.3 77.6 - - - +
32B LEU* 1.3 79.4 + - + +
33B LYS 3.4 0.2 - - - -
66B PHE* 3.8 36.3 - + - -
68B ASN* 4.0 22.0 - - + +
95B THR* 5.0 0.4 - - - -
139B MET* 5.2 0.2 - - + -
163B TRP* 3.4 56.1 - + + +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 4.0 6.1 - - - +
20B VAL* 4.8 1.6 - - + -
24B PRO* 3.9 27.8 - - + -
28B GLU* 3.0 20.8 + - + +
29B LEU* 4.0 1.1 - - + +
31B PHE* 1.3 97.1 - - + +
33B LYS* 1.3 65.9 + - - +
35B PHE* 3.5 17.9 + - + +
41B TYR* 3.8 35.2 - - + +
68B ASN* 3.9 15.5 - - - +
472D ASN 3.3 14.9 - - - +
473D VAL* 3.7 17.9 - - + -
474D PRO* 3.5 12.9 - - + +
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B HIS* 2.8 33.6 + - - +
29B LEU 2.9 9.4 + - - +
30B PRO* 2.7 39.8 + - + +
32B LEU* 1.3 76.3 - - - +
34B ASP* 1.3 85.4 + - - +
35B PHE* 3.1 1.2 + - - -
163B TRP* 4.6 0.6 - - - +
164B ASP* 2.8 33.3 + - - -
468D LEU* 5.7 2.2 - - + +
470D ALA* 3.5 37.9 - - + -
471D GLU 3.7 7.4 - - - +
473D VAL* 3.7 6.7 - - + +
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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