Contacts of the strand formed by residues 123 - 128 (chain C) in PDB entry 2POZ
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 ARG 123 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ARG* 3.4 15.2 - - - +
122C ASP* 1.3 84.8 - - + +
124C VAL* 1.3 69.4 + - - +
357C TYR* 3.3 55.0 + - + +
358C PHE 3.1 17.3 - - - +
359C GLU* 3.5 25.3 + - - +
360C MSE 3.5 3.1 - - - +
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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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121C ARG* 3.6 14.8 - - - -
123C ARG* 1.3 80.9 - - - +
125C ARG* 1.3 61.4 + - - +
319C LEU* 4.1 12.6 - - + -
322C GLU* 4.1 12.3 - - + +
328C PHE* 3.4 31.0 - - + -
331C HIS* 3.8 22.7 - - + -
357C TYR* 3.3 6.8 - - - -
358C PHE* 3.0 33.9 + - + +
360C MSE 3.5 23.3 - - + -
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Residues in contact with ARG 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 VAL* 1.3 78.1 - - - +
126C ALA* 1.3 74.1 + - - +
154C GLY* 5.4 15.0 - - - +
155C ALA* 5.6 0.2 - - - +
201C GLU* 3.3 28.1 + - - -
328C PHE* 4.6 3.8 - - - -
329C MSE 4.5 16.3 + - - +
330C ILE* 3.4 27.1 - - - +
331C HIS* 3.1 23.2 + - - +
356C GLY* 3.2 15.9 - - - +
357C TYR* 3.5 35.8 + - + -
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Residues in contact with ALA 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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125C ARG* 1.3 84.9 + - - +
127C TYR* 1.3 66.0 + - - +
153C TYR* 3.7 17.5 - - + -
154C GLY 4.5 8.1 + - - -
155C ALA* 4.6 1.0 + - - +
330C ILE* 3.6 7.6 - - - +
331C HIS* 3.1 34.1 - - + +
333C HIS* 4.5 3.1 - - + -
356C GLY* 3.0 12.5 + - - +
358C PHE* 4.0 17.0 - - + -
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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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126C ALA* 1.3 75.2 - - - +
128C ALA* 1.3 62.1 + - - +
129C ASN* 4.3 3.8 - - + -
153C TYR* 3.9 3.4 - - - -
155C ALA* 3.2 33.0 - - + +
156C LEU 4.3 0.4 - - - +
157C LYS* 3.3 48.4 + - + +
203C MSE 4.0 11.7 - - + -
229C PHE* 4.9 9.4 - + - -
278C GLN* 4.5 7.8 + - - -
305C ALA* 5.2 5.8 + - + -
306C PRO 5.2 1.1 + - - -
330C ILE* 3.6 30.0 - - + +
331C HIS 2.9 16.9 + - - -
332C GLU* 3.1 48.4 + - + +
333C HIS* 3.2 22.5 + - - +
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Residues in contact with ALA 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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127C TYR* 1.3 76.1 - - - +
129C ASN* 1.3 59.9 + - - +
131C TRP* 3.2 13.9 - - + -
148C PRO* 4.2 5.6 - - + -
153C TYR* 3.7 36.2 - - + -
155C ALA 2.9 8.3 + - - -
156C LEU* 3.7 16.0 - - + -
157C LYS 3.0 25.6 + - - -
333C HIS 3.5 5.4 - - - +
335C PRO* 4.6 6.1 - - + -
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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