Contacts of the strand formed by residues 127 - 132 (chain A) in PDB entry 3R8K
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 VAL 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A VAL* 3.5 24.9 - - + -
50A SER 3.8 3.1 - - - -
51A THR* 4.0 8.1 - - + +
68A LYS* 4.0 29.6 - - + +
69A LEU* 4.2 7.6 - - + -
72A TYR* 4.3 9.4 - - + -
122A PRO* 3.0 37.9 - - + +
124A GLU* 3.4 28.2 + - + +
125A SER 4.4 3.1 - - - +
126A ASP* 1.3 82.5 - - - +
128A PHE* 1.3 67.0 + - - +
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Residues in contact with PHE 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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49A VAL* 3.6 3.6 - - - -
50A SER* 2.8 69.5 + - - +
51A THR* 4.3 2.7 - - - -
52A SER* 4.0 24.0 - - - -
106A THR* 4.3 5.8 - - + -
122A PRO* 3.9 7.2 - - - -
126A ASP 4.1 7.9 - - - -
127A VAL* 1.3 79.3 - - - +
129A ILE* 1.3 72.9 + - - +
130A GLU* 4.4 13.9 - - + -
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Residues in contact with ILE 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* 3.7 29.8 - - + -
48A TRP 3.5 4.5 - - - +
49A VAL* 4.2 10.3 - - + -
72A TYR* 3.7 23.1 - - + +
111A ILE* 3.6 26.0 - - + -
119A PRO* 4.0 14.6 - - + +
120A PRO 4.2 3.4 - - - +
121A ARG* 5.5 0.4 - - - -
122A PRO* 4.1 17.6 - - + +
128A PHE* 1.3 81.2 - - - +
130A GLU* 1.3 64.2 + - - +
131A ASP* 3.9 3.8 + - - +
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Residues in contact with GLU 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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47A LYS* 3.1 8.8 - - - +
48A TRP* 2.4 56.8 + - + +
50A SER* 3.1 21.4 + - - +
106A THR* 5.8 1.9 - - - +
108A SER* 3.7 0.7 + - - -
128A PHE* 3.6 12.0 + - + -
129A ILE* 1.3 68.0 - - - +
131A ASP* 1.3 66.8 + - - +
132A ARG* 2.8 61.1 + - - +
175A TYR* 4.4 4.0 + - - -
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Residues in contact with ASP 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 ALA 3.8 3.1 - - - -
47A LYS* 3.1 37.1 - - - +
129A ILE* 3.9 5.4 + - - +
130A GLU* 1.3 74.4 - - - +
132A ARG* 1.3 64.2 + - - +
133A ALA* 3.3 4.0 + - - +
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Residues in contact with ARG 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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45A PRO* 3.3 3.6 - - - +
46A ALA 2.7 43.9 + - - +
48A TRP* 2.9 52.4 - - + +
90A THR* 3.5 15.4 + - - +
92A TYR* 5.4 4.4 - - - +
108A SER* 3.0 24.7 + - - -
130A GLU* 2.8 42.4 + - - +
131A ASP* 1.3 73.4 - - - +
133A ALA* 1.3 73.5 + - - +
135A MET* 4.1 17.9 - - + +
175A TYR* 3.4 34.6 + - - +
193A TRP* 5.2 1.6 - - - -
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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