Contacts of the strand formed by residues 42 - 49 (chain A) in PDB entry 4IBR
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 ARG 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLU* 3.3 2.9 - - - -
40A GLY 3.7 0.8 + - - +
41A GLY* 1.3 77.2 - - - +
43A VAL* 1.3 65.4 + - - +
60A ARG* 3.7 25.1 - - - +
63A GLU* 2.9 45.5 + - - +
64A ARG 2.8 24.9 + - - +
65A PHE* 3.4 19.6 - - + +
66A PRO* 5.5 0.4 - - - +
174A ASN* 5.7 9.3 - - - +
262A MET* 3.3 5.4 - - - +
263A THR* 2.7 56.3 + - - +
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Residues in contact with VAL 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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32A VAL* 3.5 25.8 - - + +
35A ALA* 4.2 7.0 - - + -
36A GLU* 2.8 43.3 + - + +
39A LEU* 4.5 7.0 - - + -
40A GLY 5.1 2.5 - - - +
42A ARG* 1.3 77.0 - - - +
44A GLY* 1.3 65.8 + - - +
59A PHE* 3.0 27.0 - - - -
60A ARG* 3.4 4.0 - - - -
65A PHE* 4.0 2.5 - - - -
260A ILE* 4.5 2.9 - - + -
261A TYR 3.4 8.1 - - - +
262A MET* 4.0 18.6 - - + -
279A ILE* 4.4 16.2 - - + -
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Residues in contact with GLY 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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43A VAL* 1.3 72.7 - - - +
45A TYR* 1.3 63.6 + - - +
59A PHE 3.6 7.6 - - - -
60A ARG* 4.3 1.1 - - - -
65A PHE* 3.4 25.8 - - - -
182A PRO* 4.0 7.9 - - - -
259A VAL 4.4 0.2 - - - -
260A ILE* 3.3 8.7 - - - +
261A TYR 2.7 36.9 + - - +
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Residues in contact with TYR 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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28A THR* 3.5 22.1 - - + +
29A LEU* 6.1 1.6 - - + -
32A VAL* 3.8 33.4 - - + -
43A VAL* 4.3 0.9 + - + -
44A GLY* 1.3 75.0 - - - +
46A ILE* 1.3 65.1 + - - +
47A GLU* 2.8 44.5 + - + +
57A GLU* 4.2 17.0 - - + -
58A SER* 3.2 9.2 - - - -
59A PHE* 2.9 39.5 + - + +
61A PRO* 4.7 1.0 - - - +
182A PRO* 4.0 6.1 - - - +
258A VAL* 3.7 22.7 - - + +
259A VAL 3.3 5.4 - - - -
260A ILE* 3.6 19.3 - - + -
279A ILE* 4.0 16.6 - - + -
283A LEU* 3.8 11.0 - - + +
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Residues in contact with ILE 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 TYR* 1.3 78.9 - - - +
47A GLU* 1.3 64.4 + - - +
48A LEU* 3.8 19.5 - - + -
55A ILE* 4.0 15.9 - - + -
57A GLU 3.5 12.1 - - - +
58A SER* 4.0 9.6 - - - -
61A PRO* 4.3 3.8 - - + -
182A PRO* 3.3 29.2 - - + +
183A VAL* 3.7 36.3 - - + +
186A ALA* 3.5 17.5 - - + -
257A ILE 4.3 0.2 - - - -
258A VAL* 3.4 7.8 - - - +
259A VAL* 3.0 39.7 + - + +
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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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28A THR* 4.7 5.4 + - - +
45A TYR* 2.8 28.8 + - + +
46A ILE* 1.3 77.4 - - - +
48A LEU* 1.3 58.2 + - - +
55A ILE* 3.7 3.1 - - - -
56A LEU* 2.7 48.1 + - + +
57A GLU* 2.9 23.6 + - - +
256A ARG* 2.5 46.5 + - - -
257A ILE 3.3 7.0 - - - +
258A VAL* 4.3 5.8 - - + +
283A LEU* 3.6 11.1 - - - +
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Residues in contact with LEU 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 ILE* 3.8 17.7 - - + -
47A GLU* 1.3 79.6 - - - +
49A ASP* 1.3 65.2 + - - +
53A GLY 3.7 16.8 - - - +
54A LYS 3.5 2.2 - - - -
55A ILE* 3.8 26.2 - - + -
56A LEU* 4.1 3.4 - - - -
183A VAL* 5.6 0.4 - - + -
186A ALA* 3.7 38.4 - - + +
187A THR* 4.0 11.9 - - + +
190A ARG* 4.2 17.5 - - + -
256A ARG* 3.2 10.6 - - - +
257A ILE* 2.8 43.4 + - + +
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Residues in contact with ASP 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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48A LEU* 1.3 73.2 - - - +
50A LEU* 1.3 63.6 + - - +
51A ALA* 3.9 11.2 + - - +
52A SER* 2.8 35.2 + - - +
53A GLY* 2.8 29.1 + - - -
54A LYS* 2.9 16.4 + - + +
56A LEU* 3.8 24.6 - - + +
190A ARG* 3.7 1.4 + - - -
255A SER* 3.7 9.8 - - - +
256A ARG* 5.1 1.0 - - - +
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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