Contacts of the strand formed by residues 124 - 135 (chain C) in PDB entry 4DQ0
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 THR 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C GLU* 4.0 5.7 - - - +
96C TYR 3.6 7.0 - - - +
97C ASP 5.3 0.2 - - - -
99C ILE* 3.4 6.8 - - + +
120C MET 2.7 20.6 + - - -
121C GLN 2.9 10.1 + - - -
122C ARG 4.0 0.5 - - - +
123C CYS* 1.3 79.6 - - - +
125C LYS* 1.3 74.1 + - - +
126C PRO* 4.1 1.4 - - - +
128C GLY* 3.7 20.9 - - - -
129C TYR 3.9 2.7 - - - +
130C ASN* 2.8 27.3 + - - +
163C TRP* 3.7 17.0 - - + -
196C LYS* 3.0 23.8 + - + -
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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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33C LYS* 5.5 1.5 - - - +
95C GLU* 3.9 34.1 - - + +
96C TYR 2.8 19.6 + - - +
97C ASP* 2.9 35.7 + - - +
123C CYS 4.0 0.4 + - - -
124C THR* 1.3 79.0 - - - +
126C PRO* 1.3 77.5 - - + +
127C GLY 3.4 0.2 + - - -
128C GLY* 2.8 23.6 + - - +
196C LYS* 3.6 6.1 - - - +
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Residues in contact with PRO 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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95C GLU* 5.2 2.5 - - - +
124C THR 4.1 3.6 - - - +
125C LYS* 1.3 95.6 - - + +
127C GLY* 1.3 59.0 + - - +
128C GLY 3.3 1.4 + - - -
196C LYS* 4.2 12.3 - - + +
197C LYS 3.7 22.0 - - - +
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Residues in contact with GLY 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 PRO* 1.3 71.4 - - - +
128C GLY* 1.3 58.4 + - - +
129C TYR* 3.3 10.9 - - - -
195C ARG* 2.8 43.9 + - - -
196C LYS 3.0 17.4 + - - -
197C LYS 4.3 2.2 + - - -
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Residues in contact with GLY 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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97C ASP* 3.4 18.8 - - - -
124C THR* 3.7 10.9 - - - +
125C LYS* 2.8 19.6 + - - +
126C PRO 3.1 1.8 + - - -
127C GLY* 1.3 77.1 - - - +
129C TYR* 1.3 62.3 + - - -
163C TRP* 4.2 0.2 - - - -
195C ARG* 3.3 5.7 - - - +
196C LYS* 2.9 26.4 + - - +
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Residues in contact with TYR 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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28C VAL* 3.9 38.9 + - + +
29C VAL* 3.5 31.9 - - + -
30C LYS* 6.3 1.6 - - + -
97C ASP 2.9 14.8 + - - +
98C PHE* 3.4 12.1 - - + -
99C ILE 2.9 24.7 + - - -
124C THR* 3.9 1.7 - - - +
127C GLY 3.3 18.4 - - - -
128C GLY* 1.3 76.0 - - - -
130C ASN* 1.3 67.9 + - - +
166C VAL* 4.2 11.7 - - + +
193C LEU* 4.0 15.9 - - + -
194C ALA 3.3 15.3 - - - +
195C ARG* 3.2 39.5 + - + -
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Residues in contact with ASN 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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99C ILE* 3.2 14.7 - - - +
120C MET* 3.7 25.4 - - + +
124C THR* 2.8 24.7 + - - +
129C TYR* 1.3 83.5 - - - +
131C LEU* 1.3 60.6 + - - +
132C ILE* 4.1 0.4 + - + -
160C TYR* 2.8 38.7 + - + +
163C TRP* 3.6 22.0 - - + -
192C MET* 3.6 7.4 - - + +
193C LEU* 3.6 3.0 - - - -
194C ALA* 3.0 32.1 + - - +
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Residues in contact with LEU 131 (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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21C GLU* 3.9 33.0 - - + +
22C VAL* 4.1 21.5 - - + -
25C ALA* 4.2 9.2 - - + -
98C PHE* 3.9 18.6 - - + -
99C ILE 2.8 9.2 + - - +
100C LEU* 3.3 11.9 - - + -
101C SER 2.7 32.1 + - - -
102C THR* 4.4 7.6 - - + -
120C MET* 5.1 0.3 - - - +
129C TYR 4.2 0.8 - - - -
130C ASN* 1.3 70.6 - - - +
132C ILE* 1.3 65.6 + - - +
133C VAL* 4.1 18.4 - - + -
191C THR* 5.1 2.9 - - + -
192C MET 3.2 21.3 - - - +
193C LEU* 4.0 13.0 - - + -
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Residues in contact with ILE 132 (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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101C SER* 3.4 10.3 - - - +
105C LEU* 4.0 29.2 - - + -
117C ILE* 4.9 4.0 - - + -
120C MET* 3.7 29.6 - - + -
130C ASN 5.0 0.4 - - - -
131C LEU* 1.3 81.5 - - - +
133C VAL* 1.3 74.1 + - - +
134C ALA* 4.5 1.3 - - + +
151C PHE* 4.5 2.9 - - + -
156C LEU* 3.8 37.7 - - + -
160C TYR* 3.8 15.5 - - + +
190C ALA 3.5 2.4 - - - +
192C MET* 2.9 43.7 + - + +
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Residues in contact with VAL 133 (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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19C HIS* 4.2 27.4 - - + +
21C GLU* 4.2 10.1 - - + -
101C SER 3.0 8.5 + - - +
102C THR* 4.4 6.1 - - + -
103C VAL* 2.6 51.3 + - + +
104C VAL 4.2 0.9 + - - -
105C LEU* 5.9 0.3 - - - +
131C LEU* 4.1 18.2 - - + -
132C ILE* 1.3 78.5 - - - +
134C ALA* 1.3 65.5 + - - +
189C PHE* 4.7 11.4 - - + -
190C ALA 3.3 3.6 - - - +
191C THR* 4.0 20.0 - - + +
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Residues in contact with ALA 134 (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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103C VAL* 4.7 0.7 - - - +
105C LEU* 4.5 13.5 - - + +
106C MET* 4.0 15.0 - - + +
132C ILE* 4.2 3.5 - - + +
133C VAL* 1.3 77.5 - - - +
135C ALA* 1.3 63.5 + - - +
149C PHE* 5.7 0.9 - - + -
151C PHE* 3.7 33.0 - - + -
189C PHE* 3.4 8.9 - - - -
190C ALA* 2.9 35.8 + - - +
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Residues in contact with ALA 135 (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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106C MET* 3.5 18.8 - - + +
134C ALA* 1.3 79.5 - - - +
136C MET* 1.3 61.8 + - - +
147C PHE* 3.8 31.6 - - + -
150C ALA* 3.8 6.9 - - + -
151C PHE* 3.2 19.9 + - - +
187C LEU* 3.9 9.0 - - + -
188C ARG 3.9 0.4 - - - -
189C PHE* 3.6 26.0 - - + -
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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