Contacts of the strand formed by residues 42 - 49 (chain A) in PDB entry 4O65
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 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLN* 4.4 0.5 - - - +
39A SER* 3.5 26.2 + - - +
40A ARG 5.1 0.2 - - - -
41A PHE* 1.3 85.2 - - - +
43A LYS* 1.3 63.4 + - - +
44A ILE* 4.0 2.1 + - - +
96A LEU* 3.9 13.2 - - + -
97A VAL 3.3 26.5 - - - +
98A SER* 4.2 9.6 - - - +
104A LEU* 3.6 26.9 - - + -
135A ILE* 3.9 17.5 - - + -
161A LEU* 3.6 29.3 - - + +
163A ILE* 3.9 8.5 - - + -
169A GLY* 5.6 0.9 - - - -
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Residues in contact with LYS 43 (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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36A GLN* 5.2 3.8 + - - -
38A GLN* 3.5 34.8 - - + +
39A SER 4.4 4.3 - - - +
42A VAL* 1.3 74.2 - - - +
44A ILE* 1.3 66.0 + - - +
45A GLU* 3.7 34.4 + - + +
95A ARG 3.6 0.9 - - - +
96A LEU* 3.4 4.7 - - - -
97A VAL* 2.8 35.1 + - - +
99A GLN* 4.7 20.0 + - - +
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Residues in contact with ILE 44 (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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38A GLN* 2.8 39.6 + - - +
42A VAL 4.9 1.6 - - - +
43A LYS* 1.3 73.0 - - - +
45A GLU* 1.3 61.6 + - - +
47A GLU* 4.6 7.7 + - + -
95A ARG 3.7 3.6 - - - -
96A LEU* 3.9 16.6 - - + -
143A TYR* 3.5 28.5 - - + +
159A THR* 3.7 16.6 - - + +
161A LEU* 3.9 18.8 - - + +
169A GLY* 3.5 23.8 - - - +
170A LEU 3.8 2.7 - - - -
171A GLY* 3.5 33.7 - - - +
172A PRO* 4.6 4.9 - - - +
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Residues in contact with GLU 45 (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 LYS* 3.7 37.0 - - + +
44A ILE* 1.3 77.5 - - - +
46A ASP* 1.3 76.4 + - - +
47A GLU* 3.1 4.4 + - - +
94A GLY* 3.4 1.6 - - - -
95A ARG* 2.6 66.8 + - - +
97A VAL* 3.6 29.6 - - + +
99A GLN* 5.5 2.9 + - - -
143A TYR* 4.8 0.7 - - - -
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Residues in contact with ASP 46 (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 GLU* 1.3 74.5 - - - +
47A GLU* 1.3 66.8 + - - +
48A THR* 3.4 9.9 + - - -
93A THR* 3.5 5.9 + - - +
94A GLY* 3.6 7.1 - - - -
95A ARG* 2.8 44.8 + - + +
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Residues in contact with GLU 47 (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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44A ILE* 4.6 5.4 - - + -
45A GLU 3.1 3.4 + - - -
46A ASP* 1.3 78.3 - - - +
48A THR* 1.4 61.7 + - - +
49A PHE* 3.3 25.6 - - + -
92A VAL* 3.9 4.7 - - + -
93A THR 3.2 6.7 - - - -
143A TYR* 3.7 16.2 - - - +
159A THR* 2.7 41.6 + - - +
171A GLY* 4.1 2.6 - - - -
172A PRO* 2.5 53.2 - - + +
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Residues in contact with THR 48 (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 ASP 3.5 7.8 + - - -
47A GLU* 1.4 77.0 + - - +
49A PHE* 1.3 77.4 + - - +
50A SER* 5.4 1.1 - - - -
91A ILE 3.8 0.7 - - - +
92A VAL* 3.2 6.6 - - - +
93A THR* 2.8 46.1 + - - +
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Residues in contact with PHE 49 (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 GLU* 3.3 43.1 - - + -
48A THR* 1.3 87.5 - - - +
50A SER* 1.3 65.6 + - - +
51A ALA 3.4 10.5 + - - +
90A LEU* 4.3 2.2 - - + -
91A ILE 3.5 2.9 - - - -
92A VAL* 3.7 27.1 - - + -
110A LEU* 4.5 3.1 - - + -
157A ALA* 3.4 41.5 - - + -
158A HIS* 4.5 1.1 - - - -
172A PRO 4.2 1.3 - - - -
173A GLY 4.6 0.4 - - - -
174A MET* 3.6 46.5 - - + +
176A ILE* 3.9 17.3 - - + -
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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