Contacts of the helix formed by residues 125 - 129 (chain R) in PDB entry 3EXG
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 ALA 125 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123R GLY* 3.4 4.0 - - - -
124R VAL* 1.3 84.9 - - - +
126R ALA* 1.3 66.0 + - - +
127R GLN 3.3 0.9 + - - -
128R HIS 3.5 1.9 + - - -
129R SER* 3.0 22.1 + - - -
302R MET 3.2 11.4 - - - +
303R PRO 4.4 9.6 + - - -
304R TYR* 4.5 8.9 - - + -
309R GLU* 4.4 3.4 + - - -
120S LYS 5.0 1.8 - - - +
121S GLY 3.6 19.5 - - - +
124S MET* 4.9 1.6 - - + -
125S HIS* 3.6 23.6 - - + +
103T MET* 5.8 0.4 - - + -
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Residues in contact with ALA 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125R ALA* 1.3 77.4 - - - +
127R GLN* 1.3 60.5 + - - +
128R HIS 3.2 1.6 + - - -
129R SER* 4.0 7.2 + - - -
130R GLN 4.7 1.9 + - - -
266R TRP* 5.9 0.2 - - - -
301R PRO* 3.9 22.4 - - + -
302R MET* 2.7 25.3 + - - +
120S LYS 5.7 0.2 + - - -
99T LYS* 3.3 23.0 + - + +
102T TYR* 5.4 0.2 - - + -
103T MET* 3.6 32.4 - - + +
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Residues in contact with GLN 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R ASN* 3.4 21.9 - - - +
125R ALA 3.3 1.6 + - - -
126R ALA* 1.3 75.4 - - - +
128R HIS* 1.3 74.0 + - + +
129R SER 3.7 0.4 - - - -
125S HIS* 3.3 17.6 + - + -
135S ASN* 3.9 8.9 - - - +
136S GLY* 2.9 30.7 + - - +
137S ILE* 3.7 13.8 + - + +
95T ASN* 2.5 61.1 + - - +
96T SER* 4.6 3.0 + - - +
99T LYS* 4.8 0.7 - - + -
100T THR* 5.6 0.2 + - - -
103T MET* 3.8 25.5 - - - +
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Residues in contact with HIS 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82R THR* 5.1 9.0 + - + +
84R ASN* 2.9 21.1 + - - +
85R PHE* 3.6 34.4 - + - -
119R GLY 3.9 6.2 - - - +
121R SER* 4.8 2.9 - - - -
124R VAL* 3.6 30.2 + - + +
125R ALA 3.5 1.6 + - - -
126R ALA 3.2 0.6 - - - -
127R GLN* 1.3 92.5 + - + +
129R SER* 1.3 59.3 + - - +
61S PHE* 3.8 23.2 - + + -
124S MET* 3.3 33.9 - - + +
136S GLY* 3.7 24.5 + - - -
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Residues in contact with SER 129 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84R ASN* 3.4 0.4 + - - -
119R GLY* 3.0 27.0 - - - -
120R ALA* 3.3 10.7 + - - +
121R SER 4.4 4.7 + - - -
124R VAL* 3.2 17.2 - - - +
125R ALA 3.0 22.1 + - - -
126R ALA 4.0 2.8 + - - -
127R GLN 3.7 0.4 - - - -
128R HIS* 1.3 76.5 - - - +
130R GLN* 1.3 62.2 + - - +
131R CYS* 3.8 0.7 + - - +
302R MET* 3.4 35.9 - - - +
309R GLU* 5.0 1.0 + - - -
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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