Contacts of the strand formed by residues 126 - 130 (chain C) in PDB entry 1REP
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 LEU 126 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C GLU* 4.2 18.4 - - + +
62C ILE 3.3 7.9 - - - +
63C HIS* 2.9 43.3 - - + +
121C SER* 2.9 22.3 + - - -
122C PRO* 2.9 48.8 - - + +
123C SER* 2.8 29.4 + - - +
124C ARG 3.4 0.2 - - - -
125C GLY* 1.3 81.1 - - - +
127C TYR* 1.3 64.8 + - - +
128C SER* 5.7 0.4 - - - -
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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
----------------------------------------------------------
26B A 2.5 34.8 + - - -
61C GLU* 3.1 4.2 - - - +
62C ILE* 2.6 49.1 + - + +
64C VAL* 3.5 28.5 - - + -
82C ILE* 3.8 21.8 - - + -
83C ARG* 3.1 32.3 - - + +
86C LEU* 3.8 28.3 - - + -
119C ALA* 5.6 0.2 - - + -
120C HIS* 3.5 7.6 - - - +
121C SER* 3.8 25.8 - - - -
125C GLY 4.5 0.2 - - - -
126C LEU* 1.3 79.0 - - - +
128C SER* 1.3 60.5 + - - +
129C VAL* 4.5 6.3 - - + +
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Residues in contact with SER 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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59C ILE* 4.2 14.6 - - - +
60C CYS 3.5 9.6 + - - -
61C GLU* 4.1 8.9 - - - +
118C PRO 4.8 0.2 - - - +
119C ALA* 3.7 1.6 - - - -
120C HIS* 2.8 60.7 + - - -
122C PRO* 4.1 11.8 - - - +
126C LEU* 5.8 0.4 - - - -
127C TYR* 1.3 71.6 - - - +
129C VAL* 1.3 65.9 + - - +
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PHE* 3.6 35.2 - - + -
58C GLY 3.2 0.7 - - - +
59C ILE* 3.1 3.7 - - - -
60C CYS* 2.6 54.9 + - + +
62C ILE* 5.0 2.5 - - + -
86C LEU* 4.0 26.5 - - + -
115C PHE* 4.3 11.4 - - + -
118C PRO 5.9 0.2 - - - -
119C ALA* 4.2 10.5 - - + +
127C TYR* 4.5 8.3 - - + +
128C SER* 1.3 84.2 + - - +
130C HIS* 1.3 57.3 + - - +
131C ILE* 4.1 13.7 - - + -
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Residues in contact with HIS 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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57C ASP* 3.3 26.6 + - - +
59C ILE* 3.6 31.3 - - + +
115C PHE* 3.9 6.8 - - - +
116C ILE* 3.4 46.4 + - + +
117C LYS* 3.3 42.2 + - + +
118C PRO 5.8 0.2 + - - -
119C ALA* 5.8 0.2 - - - +
129C VAL* 1.3 72.1 - - - +
131C ILE* 1.3 71.1 + - - +
132C ASN 3.2 2.9 + - - -
133C PRO* 4.0 5.4 - - + +
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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