Contacts of the helix formed by residues 4109 - 4113 (chain D) 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 GLY4109 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4107D GLY 3.6 2.8 + - - -
4108D ASP* 1.3 75.2 + - - +
4110D ASP* 1.3 69.5 + - - +
4111D TYR 3.4 0.2 + - - -
4112D GLY* 3.2 13.7 + - - -
4113D LYS* 4.9 1.1 - - - -
4114D LEU* 3.8 9.9 - - - -
4118D ASN 4.5 0.5 - - - +
4119D SER* 3.3 22.4 - - - +
4120D ASP 3.4 22.9 - - - -
4121D ARG* 3.9 7.9 - - - +
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Residues in contact with ASP4110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4135A GLU* 5.3 4.0 - - - +
4091D ASP* 4.4 1.6 - - - +
4108D ASP* 3.1 23.3 + - - +
4109D GLY* 1.3 79.0 - - - +
4111D TYR* 1.3 89.5 + - + +
4112D GLY 3.1 3.3 + - - -
4113D LYS* 3.0 20.7 + - - +
4119D SER* 4.4 9.9 - - - +
4121D ARG* 5.3 4.7 + - - +
4408D UNX 2.3 35.3 + - - -
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Residues in contact with TYR4111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4090D SER* 5.5 2.5 - - - -
4109D GLY 3.4 0.4 + - - -
4110D ASP* 1.3 94.8 + - + +
4112D GLY* 1.3 56.2 + - - +
4113D LYS* 3.4 2.9 - - - -
4119D SER* 4.1 10.6 + - - -
4144D LYS* 3.7 39.2 - - + +
4159D GLY* 3.3 20.0 - - - +
4160D ASN* 3.2 43.3 - - - +
4173D ASN* 3.7 30.5 - - - +
4174D LYS 3.6 4.0 - - - +
4175D LYS* 4.9 2.1 - - - +
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Residues in contact with GLY4112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4109D GLY 3.2 8.4 + - - -
4110D ASP 3.1 3.4 + - - -
4111D TYR* 1.3 78.4 - - - +
4113D LYS* 1.3 57.9 + - - +
4114D LEU 3.2 3.8 - - - -
4115D GLY* 3.0 21.5 + - - -
4118D ASN 3.9 12.8 - - - -
4119D SER* 4.1 2.6 + - - -
4158D PHE* 3.8 2.3 - - - -
4159D GLY* 3.9 0.2 - - - -
4174D LYS 3.4 12.9 - - - +
4175D LYS* 3.7 24.3 - - - -
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Residues in contact with LYS4113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4090D SER* 5.4 4.4 + - - -
4091D ASP* 5.5 0.4 - - - +
4092D GLY 4.8 4.5 - - - +
4093D HIS* 3.5 36.9 - - + +
4095D MET* 5.5 0.7 - - - +
4105D SER* 5.5 0.3 - - - -
4108D ASP* 2.8 52.2 + - - +
4109D GLY 4.2 0.6 + - - -
4110D ASP* 3.0 23.5 + - - +
4111D TYR* 3.4 5.3 - - - -
4112D GLY* 1.3 75.6 - - - +
4114D LEU* 1.3 58.2 + - - +
4115D GLY 3.4 0.4 - - - -
4143D PHE 4.1 8.5 - - - -
4144D LYS* 3.7 32.1 - - - +
4145D HIS* 4.1 0.7 - - - -
4146D SER* 2.8 30.7 + - - +
4158D PHE* 3.1 12.5 - - - -
4159D GLY* 3.6 12.0 - - - +
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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