Contacts of the strand formed by residues 129 - 133 (chain A) in PDB entry 4PC0
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 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU 5.5 2.8 + - - -
46A THR* 3.7 7.8 + - - +
127A VAL* 3.3 3.5 - - - -
128A ASN* 1.3 81.4 + - - +
130A ALA* 1.3 62.9 + - - +
131A ARG* 3.5 46.1 - - + +
141A ALA 3.8 0.5 - - - +
142A THR* 3.2 5.7 - - - -
143A LYS* 2.9 31.5 + - + +
181A TYR* 3.3 51.3 + - - +
182A GLY* 4.2 0.8 - - - +
183A LEU* 4.0 14.1 + - + +
231A GLU 4.9 0.8 + - - -
232A ASP* 3.9 27.1 + - - -
321A PHE 5.1 6.3 + - - -
322A GLN* 3.8 17.8 - - - +
378A SER 5.0 8.1 + - - -
379A ASP* 4.7 4.0 + - - -
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A THR* 3.1 15.7 + - + -
48A GLN* 3.8 8.0 - - - +
67A VAL* 3.7 27.0 - - + +
79A LEU* 3.9 18.8 - - + -
127A VAL* 3.9 9.9 - - + -
129A ARG* 1.3 75.1 - - - +
131A ARG* 1.3 80.8 + - - +
140A ILE* 4.1 2.5 - - + -
141A ALA 3.3 9.2 - - - +
142A THR* 4.1 0.9 - - + -
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Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A THR* 3.0 27.5 + - - -
47A ALA 3.9 10.4 + - - -
48A GLN* 3.1 31.3 - - - +
67A VAL* 5.6 0.4 - - - -
129A ARG* 3.5 29.7 - - + +
130A ALA* 1.3 81.5 + - - +
132A TYR* 1.3 59.8 + - - +
140A ILE* 4.1 4.0 - - - +
141A ALA 3.0 29.7 + - - +
183A LEU* 3.9 36.4 + - + +
184A SER* 5.8 0.7 - - - -
185A TRP* 3.1 21.3 + - + -
322A GLN* 3.7 15.0 - - - +
324A GLN* 4.6 9.7 - - - +
379A ASP* 3.1 21.4 + - - -
380A PHE 5.5 0.2 + - - -
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Residues in contact with TYR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLN* 2.9 45.8 + - + +
49A TRP 3.4 22.0 + - - -
50A LEU* 4.0 19.7 - - + -
51A PRO* 3.7 34.2 - - + +
67A VAL* 4.9 3.0 - - + +
131A ARG* 1.3 74.2 - - - +
133A MET* 1.3 72.6 + - - +
134A PRO* 3.5 27.4 - - + +
137A PRO* 3.9 22.4 - - + +
139A ILE 3.3 10.8 - - - +
140A ILE* 4.2 7.6 - - + +
185A TRP* 3.0 13.0 - - - -
384A PRO* 5.9 1.7 - - - +
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Residues in contact with MET 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A TYR* 1.3 73.6 - - - +
134A PRO* 1.3 64.7 - - + +
135A GLN* 3.6 16.6 - - + +
136A ASN* 3.0 70.4 - - + +
137A PRO 3.1 2.9 - - - -
139A ILE* 2.8 26.9 + - + +
185A TRP* 3.5 46.6 - - + +
190A SER* 3.8 19.5 - - - +
191A GLY* 3.9 14.6 - - - +
207A ILE* 4.7 4.5 - - - -
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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