Contacts of the helix formed by residues 108 - 113 (chain H) in PDB entry 4D1Q
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 PRO 108 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107G ARG* 3.8 26.2 - - - +
586G ARG* 3.9 16.2 - - - +
102H VAL* 4.4 3.4 - - - +
106H CYS 4.3 3.6 - - - +
107H ARG* 1.3 93.0 - - + +
109H PHE* 1.3 57.4 + - - +
110H SER* 3.9 2.2 - - - +
111H ALA* 2.7 36.7 + - + +
5K A 3.5 29.2 - - - +
6K A 3.4 15.7 - - - +
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Residues in contact with PHE 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G PRO* 3.4 22.6 - - + +
147G LEU* 3.8 15.1 - - + +
148G SER* 3.1 52.3 - - - -
151G VAL* 4.3 6.1 - - + -
586G ARG* 3.8 13.5 - - - -
589G ILE* 4.1 5.4 - - + -
593G THR* 3.5 24.0 - - + -
597G LEU* 3.7 16.2 - - + -
102H VAL* 4.1 24.2 - - + +
107H ARG 3.8 1.4 + - - -
108H PRO* 1.3 70.0 - - - +
110H SER* 1.3 60.7 + - - +
111H ALA 3.0 1.0 + - - -
112H VAL* 2.9 29.8 + - - +
6K A 3.0 36.7 + - + +
7K C 4.1 3.4 - - - -
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Residues in contact with SER 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G ARG* 4.2 1.5 + - - -
144G PRO* 3.5 15.2 - - - +
108H PRO* 3.9 0.9 - - - +
109H PHE* 1.3 74.7 - - - +
111H ALA* 1.3 64.8 + - - +
112H VAL 3.0 0.4 - - - -
113H SER* 2.9 19.5 + - - -
114H GLY* 3.2 9.4 + - - -
5K A 2.9 49.6 + - - -
6K A 2.9 14.6 + - - -
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Residues in contact with ALA 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G TRP* 4.7 0.7 + - - -
105G ASP* 4.1 0.2 - - - +
107G ARG* 2.8 36.1 + - - +
101H TRP* 3.6 26.7 - - + -
107H ARG* 4.6 2.2 - - + -
108H PRO* 2.7 29.1 + - + +
110H SER* 1.3 74.7 + - - +
112H VAL* 1.3 61.6 + - - +
114H GLY* 3.4 7.8 + - - -
117H PHE* 3.7 18.9 - - - +
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Residues in contact with VAL 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G LEU* 4.2 13.0 - - + +
142G PRO* 3.2 37.0 - - + +
143G SER 4.2 0.7 - - - -
144G PRO* 3.2 28.9 - - + -
147G LEU* 4.3 15.9 - - + -
98H CYS* 5.1 4.3 - - + -
101H TRP* 4.2 7.4 - - + -
109H PHE 2.9 23.6 + - - +
110H SER 3.0 1.0 - - - -
111H ALA* 1.3 78.3 - - - +
113H SER* 1.3 61.9 + - - +
117H PHE* 3.1 33.4 - - + -
118H ILE* 4.0 7.6 - - - +
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Residues in contact with SER 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G PRO 5.5 1.6 - - - -
144G PRO* 3.5 24.7 - - - +
110H SER* 2.9 16.2 + - - -
112H VAL* 1.3 77.2 - - - +
114H GLY* 1.3 68.5 + - - +
115H SER* 3.3 3.3 + - - -
118H ILE* 3.4 19.0 - - - +
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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