Contacts of the strand formed by residues 127 - 130 (chain B) in PDB entry 1A7A
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 MSE 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B ALA* 4.5 9.4 - - + -
49B ARG 3.3 3.9 + - - +
50B ILE* 4.0 11.9 - - + -
51B ALA 3.1 22.3 + - - -
125B LEU* 3.8 6.5 - - - +
126B ASN* 1.3 87.3 - - + +
128B ILE* 1.3 68.1 + - - +
129B LEU 4.2 0.4 - - - -
150B ILE* 4.4 0.9 - - - -
151B ARG* 3.5 16.4 - - + -
152B GLY* 3.5 23.6 - - - +
369B GLN* 3.5 25.4 - - - +
372B LEU* 3.6 8.3 - - - -
373B TRP* 3.0 68.2 - - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ALA 3.7 2.9 - - - -
125B LEU* 3.8 13.7 - - + -
127B MSE 1.3 80.0 - - - +
129B LEU* 1.3 61.5 + - - +
130B ASP* 3.8 7.9 - - + -
135B LEU* 3.5 19.3 - - + -
136B THR* 3.3 41.5 - - + -
139B ILE* 3.6 27.1 - - + -
140B HIS* 5.9 0.4 - - - +
147B LEU* 5.9 0.7 - - + -
150B ILE* 3.7 17.0 - - + -
152B GLY 3.1 10.5 + - - +
153B ILE* 3.5 14.8 - - + -
154B SER 2.8 27.2 + - - -
175B VAL* 5.5 1.1 - - + -
369B GLN* 3.5 7.0 + - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE* 4.0 13.2 - - + +
51B ALA 3.2 8.7 + - - +
52B GLY* 3.3 4.5 - - - -
53B CYS 3.1 24.1 + - - -
54B LEU* 4.0 22.9 - - + -
63B LEU* 4.2 4.7 - - + -
67B LEU* 3.9 29.6 - - + -
76B TRP* 3.9 12.3 - - + -
127B MSE 4.2 0.4 - - - -
128B ILE* 1.3 71.5 - - - +
130B ASP* 1.3 61.3 + - - +
135B LEU* 4.5 0.2 - - - +
154B SER 3.5 2.9 - - - +
365B GLN* 3.3 48.7 - - + +
369B GLN* 3.6 18.4 - - + +
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Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B CYS* 3.6 12.1 - - - +
128B ILE* 3.7 2.6 - - + -
129B LEU* 1.3 80.6 - - - +
131B ASP* 1.3 76.9 + - - +
133B GLY* 3.2 24.7 + - - -
134B ASP 3.7 4.3 + - - -
135B LEU* 2.9 17.8 + - - -
136B THR* 2.7 46.9 + - + +
154B SER 2.9 14.2 + - - +
155B GLU* 3.1 8.6 - - + +
156B GLU* 3.0 24.8 + - - +
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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