Contacts of the strand formed by residues 127 - 133 (chain A) in PDB entry 4RQO
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 GLY 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A TYR* 3.0 32.8 + - - +
54A LEU* 3.7 4.0 - - - +
121A LEU* 3.7 14.1 - - - -
124A HIS 4.3 0.6 + - - -
125A SER 3.4 7.7 + - - -
126A ASN* 1.3 75.8 - - - +
128A MSE 1.3 62.4 + - - -
145A TYR 3.2 9.4 - - - -
146A TYR* 3.6 14.5 - - - -
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Residues in contact with MSE 128 (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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22A GLY 4.7 0.7 - - - -
23A PRO* 3.8 26.5 - - + -
26A ALA* 3.8 17.0 - - + -
48A VAL* 5.3 1.3 - - + -
49A GLU 3.4 11.0 - - - +
50A LEU* 3.9 11.0 - - + -
51A TYR* 4.7 0.2 - - - -
54A LEU* 3.2 25.1 - - + -
67A ILE* 4.4 2.7 - - - -
121A LEU* 4.3 5.6 - - - -
127A GLY* 1.3 71.6 - - - -
129A ARG* 1.3 61.1 + - - +
130A PHE* 3.8 30.3 - - + -
144A VAL* 3.1 8.5 - - - +
145A TYR* 2.8 45.0 + - + +
146A TYR 4.3 0.4 - - - -
147A SER* 3.9 36.8 - - - +
153A ILE* 5.0 1.1 - - + -
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Residues in contact with ARG 129 (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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47A LYS 3.5 4.7 - - - +
48A VAL* 3.6 1.9 - - - +
49A GLU* 3.1 49.5 + - - +
51A TYR* 3.4 32.3 + - + -
121A LEU* 4.4 8.9 - - - +
128A MSE 1.3 76.8 - - - +
130A PHE* 1.3 67.0 + - - +
131A SER* 3.8 12.8 - - - +
142A GLU* 3.6 40.5 + - + +
143A GLN 3.5 8.5 - - - +
144A VAL* 3.8 24.7 - - + +
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Residues in contact with PHE 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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23A PRO 4.3 2.7 - - - -
26A ALA* 4.0 5.4 - - + -
27A ALA* 3.6 38.8 - - + -
30A PHE* 3.2 42.1 - + + -
46A VAL* 4.8 2.0 - - + -
47A LYS 3.4 4.7 - - - +
48A VAL* 4.1 12.8 - - + -
67A ILE* 3.8 24.7 - - + -
71A LEU* 3.9 10.5 - - + -
128A MSE 3.8 28.5 - - + -
129A ARG* 1.3 78.5 - - - +
131A SER* 1.3 60.9 + - - +
142A GLU* 3.2 2.3 - - - -
143A GLN 2.8 32.9 + - - +
145A TYR* 3.7 25.6 - + - -
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Residues in contact with SER 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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30A PHE* 3.8 2.5 - - - -
46A VAL* 3.3 6.6 - - - +
47A LYS* 2.8 41.0 + - - +
49A GLU* 4.3 6.2 + - - -
129A ARG* 3.8 11.5 - - - +
130A PHE* 1.3 73.4 - - - +
132A ALA* 1.3 58.9 + - - +
133A PHE* 3.8 24.1 - - - -
139A LEU* 3.9 11.6 - - - +
141A ILE 3.4 5.4 - - - -
142A GLU* 3.6 16.4 + - - +
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Residues in contact with ALA 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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30A PHE* 3.8 8.2 - - + -
34A LEU* 4.0 23.3 - - + -
43A THR* 3.6 24.2 - - + +
45A ARG 3.2 8.3 - - - +
46A VAL* 4.5 1.3 - - + -
131A SER* 1.3 75.0 - - - +
133A PHE* 1.3 60.5 + - - +
139A LEU* 3.6 5.2 - - - +
140A LEU* 2.9 28.1 + - + +
141A ILE* 2.9 13.2 + - + +
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Residues in contact with PHE 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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43A THR* 3.7 1.7 - - - -
44A GLN 2.8 29.8 + - - -
45A ARG* 2.7 67.5 + - + +
47A LYS* 3.7 35.0 - - + -
131A SER* 3.8 15.9 - - - -
132A ALA* 1.3 75.9 - - - +
134A ASP* 1.3 59.0 + - - +
137A ALA* 4.3 13.9 - - + -
138A ASN 3.4 10.1 - - - +
139A LEU* 3.8 33.2 - - + -
140A LEU* 3.7 5.8 - - - -
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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