Contacts of the strand formed by residues 133 - 137 (chain A) in PDB entry 3OX4
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 LEU 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 5.8 0.2 - - - -
92A VAL* 3.3 34.8 - - + +
94A SER 4.1 0.9 - - - +
101A HIS 5.1 0.2 - - - +
104A ALA* 4.0 14.8 - - + +
105A LYS* 3.8 39.5 - - + +
108A ALA* 4.4 6.7 - - + -
130A ALA* 6.0 0.4 - - + -
131A LEU 3.2 8.4 + - - +
132A PRO* 1.3 74.8 - - - +
134A MET* 1.3 70.8 + - - +
135A SER* 3.9 10.3 - - - +
168A VAL* 4.4 4.5 - - - +
170A PRO* 3.7 19.8 - - + -
171A MET* 2.8 39.6 + - - +
172A VAL 3.4 3.3 + - - -
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Residues in contact with MET 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 3.6 33.4 - - + +
23A ILE* 4.1 20.6 - - - -
26A LEU* 3.9 28.0 - - + -
91A PHE* 5.2 4.0 - - + -
92A VAL 2.9 10.4 + - - +
93A ILE* 3.1 14.0 - - + +
94A SER 2.9 25.5 + - - +
133A LEU* 1.3 75.2 - - - +
135A SER* 1.3 63.0 + - - +
136A ILE* 4.1 12.1 - - + -
172A VAL* 3.3 28.7 - - + +
174A VAL* 4.2 20.2 - - + -
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER* 2.8 21.0 + - - -
101A HIS* 3.7 7.7 + - - +
133A LEU* 3.9 8.0 + - - +
134A MET* 1.3 72.9 + - - +
136A ILE* 1.3 58.4 + - - +
137A ASN 3.8 0.7 + - - -
145A GLU* 3.6 33.0 - - - +
170A PRO* 3.3 19.6 - - - +
172A VAL 3.0 10.1 + - - -
173A SER* 3.5 1.9 - - - -
174A VAL* 2.8 31.9 + - - +
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Residues in contact with ILE 136 (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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19A LEU* 3.5 29.4 - - + -
23A ILE* 4.9 1.1 - - + -
51A VAL* 4.3 18.8 - - + -
93A ILE* 3.7 26.0 - - + -
94A SER 2.9 12.8 + - - +
95A LEU* 3.5 9.9 - - + +
96A GLY 3.0 24.8 + - - -
101A HIS* 3.3 5.5 - - - -
134A MET* 4.5 9.6 - - + -
135A SER* 1.3 73.6 - - - +
137A ASN* 1.3 60.2 + - - +
174A VAL* 3.7 22.4 - - + +
176A ASP 5.9 0.2 - - - +
179A LEU* 3.5 32.8 - - + -
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Residues in contact with ASN 137 (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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96A GLY 3.3 9.9 - - - +
97A GLY* 4.1 2.8 - - - -
98A GLY 5.0 0.3 + - - -
101A HIS* 3.7 6.5 + - - -
135A SER 3.8 1.4 + - - -
136A ILE* 1.3 75.7 - - - +
138A THR* 1.3 68.6 + - - +
139A THR* 2.6 34.1 + - - +
142A THR* 5.2 3.1 - - - +
143A ALA 4.9 0.4 - - - +
145A GLU* 3.3 28.5 + - + +
174A VAL 2.9 12.8 + - - +
175A ASN* 3.1 27.1 + - - +
176A ASP 4.6 6.2 + - - +
179A LEU* 4.6 2.1 - - - +
180A MET* 3.4 15.6 - - - +
247A GLN* 3.5 16.2 + - - +
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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