Contacts of the helix formed by residues 144 - 149 (chain K) in PDB entry 4DVQ
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 LEU 144 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129K VAL* 4.2 8.5 - - + -
140K ASN 3.4 22.4 - - - +
141K ARG* 3.1 6.0 + - - +
142K LEU 3.2 0.8 + - - -
143K ARG* 1.3 78.9 - - - +
145K ASN* 1.3 69.3 + - - +
146K PRO* 3.1 2.7 - - - -
147K ASP* 2.8 4.8 + - - +
148K VAL* 2.8 41.7 + - + +
293K LEU* 3.6 36.3 - - + -
299K LEU* 4.3 8.1 - - + -
307K ASN* 3.6 39.5 - - + +
311K LEU* 5.3 2.7 - - + -
451K LEU* 4.2 21.8 - - + -
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Residues in contact with ASN 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K ARG* 2.7 59.5 + - - +
142K LEU* 4.6 8.0 - - - +
144K LEU* 1.3 75.3 - - - +
146K PRO* 1.3 71.2 - - + +
147K ASP 3.1 0.7 + - - -
149K LEU* 3.1 20.7 + - + +
150K SER* 2.8 26.2 + - - +
447K MET* 5.1 12.1 + - - -
451K LEU* 3.1 11.8 - - - +
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Residues in contact with PRO 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K LEU 3.0 24.7 - - - +
143K ARG* 4.7 3.8 - - - -
144K LEU* 3.3 4.5 - - - +
145K ASN* 1.3 93.2 - - + +
147K ASP* 1.3 60.6 + - - +
150K SER* 2.9 29.8 + - - -
152K LYS* 5.4 3.1 - - - +
153K ALA* 3.5 6.1 + - - +
296K LYS* 4.0 21.5 - - - +
298K GLU* 5.6 2.2 - - - +
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Residues in contact with ASP 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143K ARG 5.1 1.9 - - - +
144K LEU 2.8 12.4 + - - +
146K PRO* 1.3 76.3 - - - +
148K VAL* 1.3 59.1 + - - +
153K ALA* 3.6 14.7 - - - +
156K ARG* 5.9 0.3 + - - -
286K TYR* 4.6 2.1 + - - -
289K ILE* 3.5 25.7 - - + +
292K GLU* 3.5 33.6 - - + +
293K LEU* 4.0 23.4 - - + +
296K LYS* 2.7 41.1 + - - +
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Residues in contact with VAL 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144K LEU* 2.8 43.9 + - + +
147K ASP* 1.3 78.6 - - + +
149K LEU* 1.3 58.1 + - - +
153K ALA* 4.5 2.9 - - - -
157K PHE* 3.9 19.2 - - - -
204K LEU* 5.9 0.4 - - + -
289K ILE* 3.9 24.4 - - + +
293K LEU* 5.1 1.3 - - + -
311K LEU* 4.1 20.4 - - + -
451K LEU* 3.7 38.1 - - + +
452K GLY* 4.5 8.3 - - - -
454K ARG* 5.4 0.5 - - - +
455K LEU* 5.0 6.8 + - + +
601K HEM 5.1 2.2 - - + -
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Residues in contact with LEU 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K ARG* 3.9 12.8 - - - +
145K ASN* 3.1 34.2 + - + +
147K ASP 3.8 0.2 - - - -
148K VAL* 1.3 77.9 - - - +
150K SER* 1.3 69.1 + - - +
154K VAL* 4.0 2.3 - - - +
449K GLN* 4.8 9.4 - - + +
450K CYS 3.9 13.5 - - - +
451K LEU* 3.2 23.6 - - + +
453K ARG* 4.1 11.2 - - + +
454K ARG* 2.9 62.1 + - + +
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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