Contacts of the strand formed by residues 127 - 133 (chain C) in PDB entry 4PRO
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 ALA 127 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C TYR* 6.4 0.2 - - + -
91C LEU* 3.7 11.1 - - - +
121C VAL* 3.9 0.5 - - - -
122C ASP* 2.8 31.1 + - - +
125C SER* 3.1 17.4 + - - +
126C ASN* 1.3 80.1 - - - +
128C VAL* 1.3 65.1 + - - +
129C VAL* 3.8 0.4 - - - -
152C ALA 5.7 1.1 - - - +
153C GLN* 3.8 14.4 - - - +
154C VAL 5.0 0.2 - - - -
155C ARG* 4.4 22.0 - - + +
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 3.3 35.7 - - + +
94C ALA* 3.9 12.3 - - + -
95C MET* 4.2 9.2 - - - +
98C LEU* 3.8 29.8 - - + -
120C TYR 3.5 15.7 - - - +
121C VAL* 4.3 7.6 - - + +
127C ALA* 1.3 73.9 - - - +
129C VAL* 1.3 64.4 + - - +
130C VAL* 4.8 0.4 - - + -
153C GLN 2.8 18.5 + - - +
154C VAL* 3.2 9.2 - - + +
155C ARG 2.7 28.3 + - - -
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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
----------------------------------------------------------
119C TRP* 3.0 7.4 - - - +
120C TYR* 2.7 66.7 + - + +
122C ASP* 3.7 24.9 - - + +
125C SER* 4.5 3.1 - - - +
127C ALA 3.7 0.6 + - - +
128C VAL* 1.3 73.9 - - - +
130C VAL* 1.3 66.2 + - - +
131C LYS* 3.9 18.8 - - + -
155C ARG* 3.4 36.3 - - + +
157C GLU* 4.4 12.3 - - + +
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Residues in contact with VAL 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 3.9 22.7 - - + -
116C VAL* 4.3 4.9 - - + -
118C SER 3.6 6.5 - - - +
119C TRP* 4.1 3.1 - - + -
128C VAL 4.6 0.2 - - - +
129C VAL* 1.3 79.8 - - - +
131C LYS* 1.3 61.9 + - - +
132C VAL* 4.2 17.5 - - + -
140C GLY* 4.6 5.2 - - - +
143C PHE* 4.2 20.6 - - + -
144C VAL* 4.6 5.4 - - + -
154C VAL* 3.6 26.5 - - + -
155C ARG 2.8 11.0 + - - +
156C ILE* 3.3 15.1 - - + +
157C GLU 2.9 24.6 + - - -
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Residues in contact with LYS 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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133A GLN* 3.4 22.0 + - - +
175A SER 5.6 2.8 + - - -
176A GLN 5.1 5.5 + - - -
177A ARG 4.3 8.5 + - - -
178A SER* 4.0 16.1 - - - +
116C VAL* 3.8 2.6 - - - +
117C GLN* 2.8 31.0 + - + +
118C SER* 2.8 30.2 + - - +
120C TYR* 3.4 25.1 + - + -
129C VAL* 3.9 13.5 - - + -
130C VAL* 1.3 71.9 - - - +
132C VAL* 1.3 63.0 + - - +
157C GLU* 3.2 29.4 - - + +
158C SER 5.5 0.2 - - - -
159C SER* 4.0 22.2 + - - +
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Residues in contact with VAL 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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115C GLY 3.1 13.5 - - - +
116C VAL* 4.3 4.7 - - - -
117C GLN* 4.1 4.9 - - - +
130C VAL* 4.2 7.0 - - + -
131C LYS* 1.3 80.4 - - - +
133C ASP* 1.3 73.3 + - - +
136C ALA 3.8 4.9 - - - +
137C THR* 3.6 24.7 - - - +
140C GLY* 3.7 31.6 - - - +
156C ILE* 4.1 14.6 - - + -
157C GLU 3.0 13.5 + - - +
158C SER* 4.4 7.0 - - - +
159C SER* 2.8 26.6 + - - +
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Residues in contact with ASP 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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115C GLY* 2.7 36.5 + - - +
116C VAL 5.6 0.2 - - - -
117C GLN* 3.0 27.9 + - - +
132C VAL* 1.3 79.8 - - - +
134C ASP* 1.3 70.1 + - - +
135C GLY 3.2 0.2 + - - -
136C ALA* 2.9 24.1 + - + +
158C SER* 4.1 0.5 + - - -
159C SER 3.7 6.3 - - - -
161C GLY 3.7 9.6 - - - +
162C LYS* 4.6 5.4 - - - -
163C LEU 5.0 0.2 + - - -
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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