Contacts of the helix formed by residues 445 - 449 (chain L) 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 PHE 445 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97L VAL* 4.1 22.2 - - + -
100L LEU* 4.2 29.8 - - + -
101L GLN* 3.6 46.7 - - + +
104L ASP* 3.6 11.6 - - - +
382L LEU* 3.8 25.8 - - + -
383L GLU 6.4 0.4 - - - -
384L ARG* 3.5 40.6 + - - -
405L VAL* 5.4 0.4 - - + -
441L VAL* 5.0 4.9 - - + -
443L PHE 3.8 0.8 + - - -
444L GLY* 1.3 78.4 - - - +
446L GLY* 1.3 70.1 + - - +
447L MET 3.7 0.7 + - - -
448L ARG 3.8 0.5 + - - -
449L GLN* 3.3 14.9 + - - +
601L HEM 3.2 8.7 + - - +
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Residues in contact with GLY 446 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L GLN* 3.7 27.9 + - - +
104L ASP* 4.4 4.0 - - - -
445L PHE* 1.3 80.4 - - - +
447L MET* 1.3 67.8 + - - -
449L GLN* 2.6 37.5 + - - +
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Residues in contact with MET 447 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104L ASP* 4.6 4.8 + - - -
106L LEU 5.8 0.2 - - - +
108L PRO* 4.8 8.3 - - + -
137L TRP* 3.6 25.8 - - + -
138L ARG* 4.6 20.9 - - - +
141L ARG* 3.3 29.5 + - - +
142L LEU* 5.4 9.2 - - - -
145L ASN* 5.2 14.4 + - - +
445L PHE 3.7 0.2 + - - -
446L GLY* 1.3 77.5 - - - +
448L ARG* 1.3 56.6 + - - +
449L GLN* 3.4 5.6 - - - +
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Residues in contact with ARG 448 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104L ASP* 5.3 0.2 + - - -
108L PRO* 3.3 38.2 + - + +
110L ARG* 3.5 40.1 + - - +
129L VAL 3.0 10.9 + - - -
130L PHE 3.9 1.0 + - - -
132L LEU 2.8 15.5 + - - -
133L ASN* 2.7 31.9 + - - +
137L TRP* 3.0 35.5 - - + +
141L ARG* 3.6 7.2 + - - +
384L ARG* 3.8 21.5 - - - +
445L PHE 3.8 0.4 + - - -
446L GLY 3.3 0.6 - - - -
447L MET* 1.3 76.8 - - - +
449L GLN* 1.3 66.1 + - - +
601L HEM 2.9 49.5 + - - +
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Residues in contact with GLN 449 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L ARG* 2.8 32.5 + - - +
149L LEU* 4.7 8.8 - - + +
443L PHE* 3.4 15.0 - - + +
444L GLY 4.2 1.6 - - - +
445L PHE* 3.3 15.8 + - - +
446L GLY* 2.6 32.2 + - - +
447L MET* 3.4 6.4 - - - +
448L ARG* 1.3 75.4 - - - +
450L CYS* 1.3 73.4 + - - +
453L ARG* 3.8 25.5 + - - -
454L ARG* 5.8 0.2 + - - -
601L HEM 3.8 5.2 - - - -
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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