Contacts of the helix formed by residues 2404 - 2408 (chain B) in PDB entry 1CVU
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 PHE2404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2391B LEU* 3.6 36.3 - - + -
2392B PRO 3.1 27.6 - - - -
2393B ASP* 3.8 15.0 + - - -
2395B PHE* 3.7 25.6 - + - -
2403B SER* 1.3 73.6 - - - +
2405B LYS* 1.3 63.0 + - - +
2407B PHE* 3.2 4.7 + - - -
2408B LEU* 3.1 47.5 - - + +
2441B PRO* 4.3 12.6 - - + -
2443B ALA* 3.8 32.5 - - + +
2444B VAL* 4.6 12.1 - - + -
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Residues in contact with LYS2405 (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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2403B SER* 3.1 10.4 + - - +
2404B PHE* 1.3 81.3 - - - +
2406B GLN* 1.3 62.5 + - + +
2407B PHE 3.4 2.8 + - - -
2408B LEU* 3.8 15.3 - - - +
2681B NAG 5.0 1.0 - - - +
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Residues in contact with GLN2406 (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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2401B GLU 3.9 5.1 + - - +
2402B TYR* 3.3 26.9 - - + +
2403B SER* 2.6 40.3 + - - +
2405B LYS* 1.3 80.1 - - + +
2407B PHE* 1.3 58.1 + - - +
2408B LEU 3.6 1.3 - - - -
2410B ASN* 3.9 10.7 + - - +
2413B ILE* 3.0 24.1 - - - +
2681B NAG 3.9 31.3 + - - +
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Residues in contact with PHE2407 (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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2200B PHE* 3.9 20.0 - + - -
2295B VAL* 5.4 0.7 - - + -
2296B PRO* 3.5 19.2 - - + +
2297B GLY 4.8 5.4 - - - -
2395B PHE* 3.5 49.8 - + + -
2397B ILE* 3.8 24.2 - - + -
2402B TYR* 3.8 16.8 - + + -
2403B SER 3.2 16.7 + - - +
2404B PHE 3.2 2.4 + - - +
2405B LYS 3.2 1.0 - - - -
2406B GLN* 1.3 78.1 - - - +
2408B LEU* 1.3 73.3 + - + +
2410B ASN 4.9 0.2 - - - -
2413B ILE* 3.8 25.8 - - + -
2422B PHE* 4.2 7.2 - + - -
2426B PHE* 3.8 21.1 - + - -
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Residues in contact with LEU2408 (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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2200B PHE* 6.2 0.7 - - + -
2294B LEU* 4.9 2.0 - - + -
2295B VAL* 3.7 30.3 - - + +
2296B PRO* 4.6 2.7 - - - -
2395B PHE* 5.9 3.6 - - + -
2404B PHE* 3.1 45.9 + - + +
2405B LYS* 3.8 11.7 + - - +
2406B GLN 3.6 1.4 - - - -
2407B PHE* 1.3 93.8 - - + +
2409B TYR* 1.3 72.4 + - + +
2410B ASN* 3.3 5.1 + - - +
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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