Contacts of the strand formed by residues 123 - 130 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C LEU* 3.6 24.1 - - - +
121C GLY 3.0 11.0 - - - +
122C GLY* 1.3 79.6 - - - +
124C GLY* 1.3 60.3 + - - +
153C GLU* 3.5 34.7 + - + +
154C ILE* 3.4 8.4 - - - +
184C ASP* 4.7 2.6 - - - +
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Residues in contact with GLY 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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120C LEU* 4.7 3.4 - - - -
123C LYS* 1.3 78.7 - - - +
125C LYS* 1.3 63.9 + - - -
153C GLU 3.7 8.1 + - - +
154C ILE* 3.4 9.9 - - - +
155C GLU* 2.9 31.9 + - - +
184C ASP* 3.2 11.7 - - - -
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Residues in contact with LYS 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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124C GLY* 1.3 75.0 - - - -
126C VAL* 1.3 62.6 + - - +
155C GLU* 3.5 25.8 - - + +
157C VAL* 3.8 23.3 - - + -
180C HIS* 4.3 14.7 + - - +
182C ASP* 3.1 41.4 + - - +
183C LEU* 3.6 15.4 - - + +
184C ASP* 2.5 36.1 + - - +
185C ALA 3.5 6.6 + - - -
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Residues in contact with VAL 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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116C MET* 4.2 13.9 - - + -
120C LEU* 3.8 25.1 - - + -
125C LYS* 1.3 79.4 - - - +
127C VAL* 1.3 79.2 + - - +
128C ILE* 4.5 3.4 - - + +
145C PHE* 4.0 24.7 - - + -
154C ILE* 4.3 12.1 - - + -
155C GLU 3.1 11.9 + - - +
156C ILE* 3.5 9.2 - - + +
157C VAL* 3.0 27.8 + - - +
158C ASP 3.7 0.3 + - - -
185C ALA* 3.3 13.9 - - + +
186C PHE 4.7 0.2 - - - -
187C PHE* 4.3 9.6 - - + +
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Residues in contact with VAL 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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126C VAL* 1.3 79.3 - - - +
128C ILE* 1.3 65.4 + - - +
157C VAL* 3.9 10.5 - - + -
158C ASP* 3.5 16.4 - - + +
160C LEU* 3.5 32.3 - - + -
176C ALA* 4.0 10.8 - - + +
180C HIS* 5.0 3.6 - - + -
183C LEU* 3.4 34.3 - - + -
185C ALA 3.1 4.2 + - - -
186C PHE* 3.3 26.3 - - + -
187C PHE 2.9 24.6 + - - -
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Residues in contact with ILE 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 VAL* 4.6 6.3 - - + -
127C VAL* 1.3 80.4 - - - +
129C GLY* 1.3 65.6 + - - +
130C THR 4.5 0.4 - - - +
142C ILE* 4.2 29.8 - - + -
145C PHE* 4.5 8.3 - - + -
156C ILE* 3.7 26.7 - - + -
158C ASP 2.7 15.9 + - - +
159C ILE* 3.7 29.6 - - + -
160C LEU* 2.9 28.9 + - - +
187C PHE* 3.5 18.8 - - + +
189C VAL* 3.7 27.6 - - + -
197C GLN* 4.5 0.4 - - - -
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Residues in contact with GLY 129 (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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128C ILE* 1.3 74.1 - - - +
130C THR* 1.3 60.8 + - - -
160C LEU* 3.6 7.0 - - - -
187C PHE 3.0 9.7 + - - -
189C VAL* 2.9 28.2 + - - +
193C ASN* 2.7 23.2 - - - +
197C GLN* 3.6 11.5 - - - +
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Residues in contact with THR 130 (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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128C ILE* 4.8 0.2 - - - -
129C GLY* 1.3 76.1 - - - -
131C GLY* 1.3 67.3 + - - +
132C SER 3.2 20.7 + - - +
133C LEU* 4.4 8.5 - - + -
138C SER* 2.7 26.9 + - - +
142C ILE* 4.4 3.6 - - + -
159C ILE* 4.4 12.8 - - + -
160C LEU 3.0 15.2 + - - +
161C ASN* 3.4 10.2 - - + -
162C ASP* 2.8 30.0 + - - +
189C VAL* 3.9 16.7 - - - +
190C TYR* 4.0 1.8 - - - +
193C ASN* 3.1 10.5 - - - +
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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