Contacts of the strand formed by residues 123 - 131 (chain C) in PDB entry 4TZQ
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 GLU 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C ARG* 2.9 41.9 + - - +
110C LEU 4.0 0.3 - - - +
112C ILE* 2.8 51.2 + - + +
121C ALA 3.5 0.8 - - - -
122C ILE* 1.3 90.8 - - + +
124C VAL* 1.3 68.2 + - - +
125C PHE* 3.3 28.3 - - + -
186C LEU* 3.5 4.4 - - - +
189C LEU* 4.0 3.0 - - + +
223C LEU* 5.7 0.2 - - - -
227C ILE* 5.3 0.4 - - - -
246C CYS* 4.8 0.4 - - - -
247C TRP 3.2 13.7 - - - +
248C SER* 2.7 26.5 + - - +
250C LEU* 4.2 0.9 - - - +
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Residues in contact with VAL 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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109C SER* 4.3 4.9 - - - -
110C LEU 3.5 6.1 - - - +
111C VAL* 4.3 9.4 - - + -
121C ALA* 3.6 22.0 - - + -
123C GLU* 1.3 80.6 - - - +
125C PHE* 1.3 77.7 + - - +
126C SER* 3.9 3.6 - - - +
221C TYR* 3.8 37.2 - - + +
223C LEU* 4.0 4.9 - - + -
246C CYS* 3.4 4.2 - - - +
247C TRP* 2.6 64.3 + - + +
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Residues in contact with PHE 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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50C PHE* 3.4 20.2 - - + -
53C VAL* 3.6 44.2 - - + -
57C ARG* 4.7 8.1 - - + -
59C ILE* 5.6 0.2 - - + -
109C SER* 3.3 3.5 - - - -
110C LEU* 3.0 43.8 + - + +
112C ILE* 4.8 5.8 - - + -
123C GLU* 3.3 32.5 - - + -
124C VAL* 1.3 76.3 - - - +
126C SER* 1.3 58.3 + - - +
178C VAL* 5.5 2.7 - - + -
181C LEU* 5.3 3.6 - - + -
182C CYS* 4.9 6.7 - - - -
186C LEU* 4.2 13.2 - - + -
232C ILE* 3.9 19.3 - - + -
244C MET* 4.8 3.1 - - + -
245C GLU 3.6 2.9 - - - +
246C CYS* 3.9 24.9 - - + -
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Residues in contact with SER 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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107C GLU* 3.6 12.8 - - - -
109C SER* 3.2 17.7 - - - -
124C VAL* 3.9 12.5 - - - +
125C PHE* 1.3 74.5 - - - +
127C MET* 1.3 61.0 + - - +
128C LYS* 4.0 12.3 - - - +
221C TYR* 4.1 1.6 - - - -
243C ASN 3.5 0.9 - - - +
244C MET* 3.2 7.2 - - - +
245C GLU* 2.9 40.0 + - - +
247C TRP* 3.3 19.7 + - - -
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Residues in contact with MET 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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42C MET* 4.4 0.7 - - + -
45C ALA 4.9 1.6 - - - +
46C ILE* 4.0 23.1 - - + +
49C ALA* 4.3 4.5 - - + -
50C PHE* 3.4 35.7 - - + -
107C GLU* 3.3 3.6 - - - +
108C VAL* 3.0 36.1 + - + +
126C SER* 1.3 77.4 - - - +
128C LYS* 1.3 62.6 + - - +
129C PHE* 3.2 32.5 - - + -
174C ILE* 5.9 0.2 - - + -
235C LEU* 4.1 25.6 - - + -
242C ALA* 4.5 5.8 - - + -
243C ASN 3.5 4.3 - - - +
244C MET* 3.9 30.1 - - + +
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Residues in contact with LYS 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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106C LYS 3.5 4.3 - - - +
107C GLU* 3.4 34.3 + - + +
126C SER* 4.0 17.3 - - - +
127C MET* 1.3 76.2 - - - +
129C PHE* 1.3 62.7 + - - +
151C PRO* 4.6 17.2 - - - +
152C HIS* 3.5 42.8 - - + +
156C LEU* 3.6 4.2 - - - +
221C TYR* 4.5 5.7 + - - -
242C ALA* 3.2 4.9 - - - +
243C ASN* 3.0 36.3 + - + +
245C GLU* 4.3 10.3 + - - +
247C TRP* 4.3 17.2 - - - -
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Residues in contact with PHE 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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42C MET* 3.3 35.7 - - + -
46C ILE* 3.7 30.5 - - + -
100C THR* 4.4 14.4 - - + -
105C LEU* 3.5 40.3 - - + +
106C LYS* 2.8 22.7 + - - +
108C VAL* 3.8 7.4 - - + -
127C MET* 3.2 40.8 - - + -
128C LYS* 1.3 74.7 - - - +
130C ILE* 1.3 62.9 + - - +
131C TYR* 3.9 13.5 - + + +
142C SER* 5.0 1.2 + - - -
152C HIS* 3.0 16.6 + - - -
202C THR* 5.9 0.2 - - - +
240C HIS* 6.1 2.0 - - + -
241C ALA 3.4 6.1 - - - +
242C ALA* 3.9 7.9 - - + -
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Residues in contact with ILE 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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129C PHE* 1.3 72.2 - - - +
131C TYR* 1.3 78.6 + - - +
132C PHE* 3.4 28.9 - - + -
139C ALA* 4.8 2.5 - - + -
140C ARG 4.6 2.5 - - - +
142C SER* 3.6 17.3 - - - -
152C HIS* 3.2 31.2 - - + +
153C PHE* 3.5 46.0 - - + +
156C LEU* 4.1 15.2 - - + +
157C ALA 4.8 0.9 - - - +
240C HIS* 3.9 2.4 - - - +
241C ALA* 2.9 35.2 + - + +
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Residues in contact with TYR 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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100C THR* 3.2 33.3 - - - -
103C GLY* 3.4 33.4 - - - -
105C LEU* 2.4 50.0 + - - +
129C PHE* 3.9 16.3 - + + +
130C ILE* 1.3 81.8 - - - +
132C PHE* 1.3 67.6 + - - +
139C ALA* 3.5 7.1 - - - +
140C ARG* 2.9 50.8 + - + +
202C THR* 4.0 8.5 - - + -
204C ASP* 6.0 0.2 - - - -
239C CYS 4.6 1.3 - - - -
240C HIS* 3.6 23.8 - + + -
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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