Contacts of the strand formed by residues 121 - 127 (chain G) in PDB entry 1DE4
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 GLN 121 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117G GLY* 3.3 1.8 - - - -
118G TYR* 3.0 28.3 + - - +
119G ASP* 4.0 5.9 - - - +
120G GLY* 1.3 86.7 - - - +
122G ASP* 1.3 71.4 + - - +
123G HIS* 3.2 0.7 + - - +
137G GLU* 4.6 12.8 - - - +
1H ILE* 2.8 44.4 + - + +
3H ARG* 4.6 2.6 - - - +
60H TRP* 4.0 7.7 - - - -
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Residues in contact with ASP 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G LYS* 5.2 11.3 - - - +
116G TYR 4.2 2.9 - - - -
121G GLN* 1.3 75.0 - - - +
123G HIS* 1.3 57.4 + - - +
136G ALA* 3.1 26.1 - - + +
137G GLU* 3.4 14.9 - - - +
58H LYS 5.1 1.2 - - - +
60H TRP* 2.7 30.5 + - - +
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Residues in contact with HIS 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G ILE* 3.7 23.3 - - + +
87G HIS* 3.2 39.9 - + - -
96G LEU* 6.0 0.2 - - + -
116G TYR* 3.1 17.2 + - + +
118G TYR* 3.8 25.0 - - + +
121G GLN 4.0 0.2 - - - +
122G ASP* 1.3 74.3 - - - +
124G LEU* 1.3 92.1 + - + +
135G ALA* 3.4 2.9 - - - -
136G ALA* 2.7 30.0 + - - +
137G GLU* 4.0 14.9 + - - -
139G ARG 4.0 0.7 - - - -
140G ALA* 3.3 34.4 + - + +
143G THR* 4.8 2.2 + - - -
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Residues in contact with LEU 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G ILE* 4.1 4.7 - - + -
115G LYS* 3.6 3.1 - - - +
116G TYR* 2.9 42.7 + - + +
123G HIS* 1.3 109.5 - - + +
125G GLU* 1.3 59.8 + - - +
126G PHE 4.2 0.4 - - - -
133G TRP* 4.1 21.8 - - + -
134G ARG 3.5 2.0 - - - -
135G ALA* 4.2 8.3 - - - -
136G ALA* 6.0 0.4 - - - -
140G ALA* 4.0 16.4 - - + +
143G THR* 3.6 26.9 - - + -
144G LYS* 4.0 22.7 - - + -
147G TRP* 4.1 15.5 - - + -
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Residues in contact with GLU 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LYS* 3.4 27.5 + - - -
114G TRP 3.9 3.4 - - - +
115G LYS* 3.0 43.2 + - + +
124G LEU* 1.3 74.9 - - - +
126G PHE* 1.3 72.7 + - - +
127G CYS* 3.5 9.5 + - - -
133G TRP* 3.4 4.1 - - - -
134G ARG* 3.0 64.3 + - + +
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Residues in contact with PHE 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G TYR* 5.5 1.8 - - - -
114G TRP* 3.0 36.0 + - + +
124G LEU 4.2 0.2 - - - -
125G GLU* 1.3 78.9 - - - +
127G CYS* 1.3 69.2 + - - +
128G PRO* 3.2 51.1 - - + +
131G LEU* 4.4 2.5 - - - -
132G ASP 3.4 14.6 - - - -
133G TRP* 3.4 41.9 - + - +
154G ALA* 3.6 34.1 - - + -
157G ASN* 3.9 17.3 - - + -
158G ARG* 3.9 8.1 - - + -
161G LEU* 3.8 19.3 - - + -
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Residues in contact with CYS 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G GLU* 3.7 18.4 - - - -
126G PHE* 1.3 76.9 - - - +
128G PRO* 1.3 66.1 - - - +
129G ASP* 3.4 2.7 - - + +
130G THR* 3.3 17.5 + - - +
131G LEU* 3.1 18.5 + - - -
132G ASP* 2.8 26.1 + - - +
134G ARG* 4.2 28.9 - - - -
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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