Contacts of the strand formed by residues 123 - 130 (chain D) in PDB entry 3C6Q
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 LYS 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLN* 5.5 1.6 - - - +
297A GLU 5.4 1.0 + - - -
300A GLY* 4.0 30.6 + - - -
301A ILE 6.0 0.2 - - - -
302A PRO* 4.5 12.8 - - + -
120D LEU* 3.6 24.3 - - - +
121D GLY 3.0 10.5 - - - +
122D GLY* 1.3 79.2 - - - +
124D GLY* 1.3 60.5 + - - +
153D GLU* 3.5 34.7 + - + +
154D ILE* 3.4 8.4 - - - +
184D ASP* 4.7 2.3 - - - +
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Residues in contact with GLY 124 (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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120D LEU* 4.7 3.4 - - - -
123D LYS* 1.3 78.2 - - - +
125D LYS* 1.3 64.4 + - - -
153D GLU 3.7 8.2 + - - +
154D ILE* 3.4 9.6 - - - +
155D GLU* 2.9 32.4 + - - +
184D ASP* 3.2 11.4 - - - -
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Residues in contact with LYS 125 (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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124D GLY* 1.3 75.6 - - - -
126D VAL* 1.3 64.9 + - - +
155D GLU* 3.5 25.6 - - + +
157D VAL* 3.8 23.1 - - + -
180D HIS* 4.3 14.7 + - - +
182D ASP* 3.1 41.0 + - - +
183D LEU* 3.7 16.2 - - + +
184D ASP* 2.5 35.8 + - - +
185D ALA 3.4 6.8 + - - -
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Residues in contact with VAL 126 (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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116D MET* 4.2 13.9 - - + -
120D LEU* 3.8 24.9 - - + -
125D LYS* 1.3 80.3 - - - +
127D VAL* 1.3 78.7 + - - +
128D ILE* 4.5 3.4 - - + +
145D PHE* 4.0 25.1 - - + -
154D ILE* 4.3 12.3 - - + -
155D GLU 3.1 11.5 + - - +
156D ILE* 3.6 8.9 - - + +
157D VAL* 3.0 27.7 + - - +
158D ASP 3.7 0.3 + - - -
185D ALA* 3.3 13.9 - - + +
186D PHE 4.7 0.2 - - - -
187D PHE* 4.3 9.2 - - + +
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Residues in contact with VAL 127 (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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126D VAL* 1.3 78.7 - - - +
128D ILE* 1.3 65.2 + - - +
157D VAL* 3.9 10.3 - - + -
158D ASP* 3.5 16.4 - - + +
160D LEU* 3.5 32.8 - - + -
176D ALA* 4.0 11.0 - - + +
180D HIS* 5.0 3.4 - - + -
183D LEU* 3.4 34.8 - - + -
185D ALA 3.1 4.2 + - - -
186D PHE* 3.3 25.1 - - + -
187D PHE 2.9 24.8 + - - -
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Residues in contact with ILE 128 (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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126D VAL* 4.6 4.3 - - + -
127D VAL* 1.3 81.6 - - - +
129D GLY* 1.3 66.2 + - - +
130D THR 4.6 0.4 - - - +
142D ILE* 4.1 29.8 - - + -
145D PHE* 4.5 8.3 - - + -
156D ILE* 3.7 34.5 - - + -
158D ASP 2.6 15.7 + - - +
159D ILE* 3.7 21.1 - - + -
160D LEU* 2.9 28.2 + - - +
187D PHE* 3.5 20.4 - - + +
189D VAL* 3.7 27.1 - - + -
197D GLN* 4.5 0.7 - - - -
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Residues in contact with GLY 129 (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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128D ILE* 1.3 74.4 - - - +
130D THR* 1.3 61.8 + - - -
160D LEU* 3.6 7.0 - - - -
187D PHE 3.0 9.7 + - - -
189D VAL* 2.9 28.1 + - - +
193D ASN* 2.7 23.3 + - - +
197D GLN* 3.6 11.3 - - - +
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Residues in contact with THR 130 (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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128D ILE* 4.8 0.2 - - - -
129D GLY* 1.3 75.7 - - - -
131D GLY* 1.3 66.5 + - - +
132D SER 3.2 20.7 + - - +
133D LEU* 4.3 8.7 - - + -
138D SER* 2.7 26.9 + - - +
142D ILE* 4.4 3.1 - - + -
159D ILE* 4.4 12.8 - - + -
160D LEU 2.9 18.6 + - - +
161D ASN* 3.4 10.0 - - + -
162D ASP* 2.8 30.7 + - - +
189D VAL* 3.9 17.4 - - - +
190D TYR* 4.0 1.1 - - - +
193D ASN* 3.1 10.9 - - - +
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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