Contacts of the strand formed by residues 4174 - 4179 (chain C) in PDB entry 4O2W
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 LYS4174 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4111C TYR 3.8 1.0 - - - +
4112C GLY 3.8 0.5 - - - +
4158C PHE* 3.5 5.7 - - - +
4159C GLY* 2.7 40.0 + - - -
4166C LEU* 3.8 9.6 - - + -
4168C LEU* 3.7 28.3 - - + -
4170C ASN* 3.7 31.7 - - - +
4172C SER* 3.7 14.2 - - - +
4173C ASN* 1.3 79.0 - - - +
4175C LYS* 1.3 64.2 + - - +
4176C LEU 3.4 3.1 - - - +
4178C GLU* 3.7 32.9 + - + +
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Residues in contact with LYS4175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4111C TYR* 4.6 7.0 - - - +
4112C GLY* 3.7 21.3 - - - +
4115C GLY* 3.2 14.7 - - - -
4116C HIS 3.4 0.3 + - - -
4117C GLY* 2.9 36.3 + - - +
4118C ASN* 3.7 23.3 - - - +
4119C SER* 3.2 28.1 + - - +
4173C ASN* 4.4 9.7 + - - +
4174C LYS* 1.3 75.3 - - - +
4176C LEU* 1.3 61.3 + - + +
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Residues in contact with LEU4176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4115C GLY 3.9 7.9 - - - +
4116C HIS 4.1 2.7 - - - -
4117C GLY* 3.5 31.4 - - - +
4130C ALA* 4.4 13.5 - - + -
4158C PHE* 3.4 11.8 - - - +
4174C LYS* 3.9 1.6 - - - +
4175C LYS* 1.3 79.0 - - + +
4177C PRO* 1.3 76.3 - - + +
4178C GLU* 3.2 28.3 + - - +
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Residues in contact with PRO4177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4115C GLY* 3.7 17.5 - - - +
4128C ILE* 3.9 15.5 - - + -
4130C ALA* 3.7 16.5 - - + +
4131C LEU* 3.7 31.9 - - + -
4156C PHE* 4.0 16.6 - - + -
4158C PHE* 3.6 29.2 - - + -
4176C LEU* 1.3 87.3 - - + +
4178C GLU* 1.3 63.6 + - - +
4179C ARG 4.1 0.5 + - - -
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Residues in contact with GLU4178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4156C PHE* 3.3 4.5 - - - -
4157C THR* 2.8 39.0 + - - +
4168C LEU* 3.9 20.4 - - + +
4174C LYS* 3.7 37.8 + - + +
4176C LEU* 3.4 31.4 + - - +
4177C PRO* 1.3 76.9 - - - +
4179C ARG* 1.3 66.7 + - - +
4180C VAL 3.4 0.7 + - - -
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Residues in contact with ARG4179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4153C GLY 4.7 3.2 + - - -
4154C LYS* 3.7 40.7 - - - +
4155C LEU* 3.4 30.6 + - - +
4156C PHE* 3.7 23.4 - - + -
4168C LEU* 3.5 10.9 - - - +
4177C PRO 4.1 0.2 + - - -
4178C GLU* 1.3 74.9 + - - +
4180C VAL* 1.3 80.6 + - - +
4181C THR* 3.1 24.9 + - - +
4183C LEU* 4.3 11.1 + - - +
4184C GLU* 3.6 37.5 + - + +
4186C TYR 5.1 0.8 + - - -
4188C ILE* 5.8 0.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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