Contacts of the helix formed by residues 926 - 932 (chain C) in PDB entry 4OIP
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 926 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922C PHE* 2.8 38.8 + + + +
925C TYR* 1.3 84.2 - + + +
927C GLY* 1.3 52.4 + - - +
928C LYS 3.0 4.5 - - - -
929C ARG* 2.6 72.8 + - - +
930C LYS* 3.4 31.3 + - + -
936C VAL* 3.8 21.5 - - + -
960C GLU* 3.5 47.6 - - + -
963C LEU* 3.6 21.1 - - + -
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Residues in contact with GLY 927 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922C PHE 4.0 0.4 + - - -
923C GLU* 3.3 23.6 + - - +
926C PHE* 1.3 79.7 - - - +
928C LYS* 1.3 61.5 + - - +
929C ARG 3.3 0.2 - - - -
930C LYS* 3.6 20.6 + - - +
931C GLY* 3.6 8.0 + - - -
960C GLU* 5.3 3.1 + - - -
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Residues in contact with LYS 928 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896C PHE* 6.1 2.8 - - - -
923C GLU 3.9 1.8 + - - -
924C VAL* 3.3 38.5 + - - +
925C TYR 4.8 3.4 - - - +
926C PHE 4.4 0.7 - - - +
927C GLY* 1.3 76.9 - - - +
929C ARG* 1.3 62.9 + - - +
930C LYS 3.4 0.2 + - - -
931C GLY* 3.5 3.3 + - - -
932C GLU* 3.1 48.4 + - + +
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Residues in contact with ARG 929 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLN* 3.4 30.1 + - - +
198A ARG* 6.2 0.2 - - - +
862C PRO* 3.4 31.0 - - - +
863C ASP* 5.2 0.8 - - - +
925C TYR* 4.8 5.3 + - - +
926C PHE* 2.6 56.6 + - - +
928C LYS* 1.3 74.9 - - - +
930C LYS* 1.3 65.1 + - + +
932C GLU* 3.0 29.2 + - - +
934C PHE* 3.3 34.7 + - + +
935C GLY 4.2 5.4 + - - -
936C VAL* 4.4 0.8 - - - +
937C ASP* 5.1 0.8 - - - +
940C GLU* 2.8 35.2 + - - -
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Residues in contact with LYS 930 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926C PHE* 3.5 45.4 - - + +
927C GLY* 3.9 11.0 - - - +
928C LYS 3.3 0.6 - - - -
929C ARG* 1.3 78.0 - - + +
931C GLY* 1.3 62.0 + - - +
933C GLY* 3.5 11.4 + - - -
934C PHE 3.7 9.8 + - - +
935C GLY* 3.4 30.1 - - - -
936C VAL* 4.1 5.1 - - - +
960C GLU* 4.6 11.9 - - - +
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Residues in contact with GLY 931 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927C GLY 3.6 6.5 + - - -
928C LYS 3.5 6.5 + - - -
929C ARG 3.3 0.4 - - - -
930C LYS* 1.3 74.9 - - - +
932C GLU* 1.3 60.7 + - - +
933C GLY* 3.1 6.9 + - - -
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Residues in contact with GLU 932 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLU* 4.5 5.1 - - - +
198A ARG* 3.0 33.3 + - - +
200A TRP* 6.1 0.2 - - - -
928C LYS* 3.1 40.3 + - + +
929C ARG* 3.0 22.0 + - - +
931C GLY* 1.3 78.9 - - - +
933C GLY* 1.3 56.2 + - - +
934C PHE* 3.4 22.4 - - + -
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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