Contacts of the strand formed by residues 121 - 128 (chain C) in PDB entry 3DC5
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 GLY 121 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C VAL* 3.9 9.2 - - - +
119C GLY 3.9 0.4 + - - -
120C SER* 1.3 77.0 - - - +
122C TRP* 1.3 65.2 + - - -
139C CYS 3.2 13.9 - - - -
141C ASN 3.7 11.7 - - - -
156C VAL* 2.9 30.3 + - - +
157C TRP* 3.4 13.0 - - - +
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Residues in contact with TRP 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ASN* 3.4 44.8 - - + +
74C HIS* 3.7 18.8 - + - -
77C PHE* 3.7 30.3 - + + -
117C VAL* 4.2 1.6 - - - +
121C GLY* 1.3 75.5 - - - -
123C GLY* 1.3 60.0 + - - +
124C TRP* 3.6 33.2 - + + +
138C THR* 3.1 9.5 - - - -
139C CYS* 2.9 33.0 + - + +
141C ASN 3.2 22.0 + - - -
142C GLN* 2.9 20.9 + - - -
143C ASP 5.3 3.1 - - - -
153C GLY 4.5 1.3 - - - -
154C ILE 3.3 12.6 - - - -
155C ASP* 3.5 51.8 + - + -
156C VAL* 4.1 5.8 - - - +
157C TRP* 3.9 1.2 - - - +
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Residues in contact with GLY 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LEU* 4.0 7.0 - - - -
114C THR* 3.3 27.4 + - - +
122C TRP* 1.3 74.7 - - - +
124C TRP* 1.3 61.4 + - - -
137C ALA 3.6 5.8 - - - -
138C THR* 4.3 3.6 - - - -
152C PHE 3.9 0.4 - - - +
153C GLY* 3.2 4.5 - - - -
154C ILE* 2.8 35.9 + - - +
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Residues in contact with TRP 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ASN* 3.9 27.2 + - + -
76C ILE* 3.8 35.4 - - + -
77C PHE 5.2 0.4 - - - -
80C ASN* 4.9 0.2 - - - -
110C LEU* 3.7 7.3 - - - +
122C TRP* 3.6 37.9 - + + +
123C GLY* 1.3 73.8 - - - -
125C LEU* 1.3 58.9 + - - +
126C GLY 3.9 0.6 + - - +
135C LYS 3.9 0.2 - - - +
136C ILE* 3.2 9.4 - - - +
137C ALA 2.8 39.6 + - - +
139C CYS* 3.7 29.1 - - - +
143C ASP 5.0 0.8 + - - -
145C LEU* 3.8 36.1 - - + +
148C MET* 5.7 0.4 - - - +
150C PRO* 3.7 26.0 - - + -
152C PHE* 3.3 13.2 - - - -
153C GLY* 3.3 33.0 - - - -
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU* 5.1 5.6 - - + -
96C ILE* 5.2 0.4 - - + -
100C PHE* 4.3 0.9 - - + -
106C LEU* 4.0 38.6 - - + -
110C LEU* 4.1 13.8 - - + +
124C TRP* 1.3 74.5 - - - +
126C GLY* 1.3 65.2 + - - +
134C LEU* 4.2 19.5 - - + -
135C LYS 3.6 13.2 - - - +
136C ILE* 4.2 2.5 - - + -
150C PRO* 3.9 1.6 - - - +
151C LEU* 2.8 45.0 + - + +
152C PHE* 2.8 24.8 + - + +
177C TRP* 6.0 0.9 - - + -
182C TRP* 4.9 8.7 - - + -
185C ILE* 4.5 13.5 - - + -
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Residues in contact with GLY 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C TRP 3.9 0.8 - - - -
125C LEU* 1.3 74.4 - - - +
127C TYR* 1.3 60.9 + - - -
134C LEU* 3.3 8.8 - - - +
135C LYS 2.8 34.4 + - - +
145C LEU* 4.4 2.7 - - - +
148C MET* 3.7 18.7 - - - -
149C VAL 3.1 12.8 - - - -
151C LEU* 4.0 6.3 - - - -
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Residues in contact with TYR 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C THR* 5.1 3.4 - - + -
98C ARG* 6.0 0.2 - - - -
126C GLY* 1.3 73.6 - - - -
128C CYS* 1.3 66.3 + - - +
129C LYS* 3.5 14.1 + - + -
132C LYS* 3.2 48.6 + - + +
133C ILE* 3.6 14.1 - - - -
134C LEU* 3.9 11.9 - - + -
148C MET* 3.4 3.9 - - - +
149C VAL* 2.8 38.6 + - - +
151C LEU* 4.0 12.3 - - + +
189C PHE* 3.9 17.9 - + + -
192C ALA* 3.6 45.3 - - + -
193C ARG* 3.6 28.7 + - + +
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Residues in contact with CYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C GLY 4.1 0.6 - - - -
127C TYR* 1.3 73.1 - - - +
129C LYS* 1.3 62.5 + - - +
130C LYS* 4.1 9.4 - - - -
131C ASP* 3.9 22.0 - - - -
132C LYS* 2.8 30.0 + - - -
133C ILE* 2.8 19.6 + - + +
135C LYS* 3.6 40.8 - - + -
147C GLY 4.4 11.4 - - - -
148C MET* 4.0 10.4 - - + +
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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
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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