Contacts of the strand formed by residues 39 - 45 (chain A) in PDB entry 1R6W
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ARG* 3.3 6.6 - - - +
36A GLU* 3.1 38.4 + - + +
37A GLY 3.2 0.9 - - - +
38A GLU* 1.3 89.3 - - + +
40A GLU* 1.3 61.8 + - - +
93A GLU 4.4 3.1 + - - -
94A LEU* 2.9 39.0 + - + +
95A THR* 4.1 2.4 + - - +
96A ASP* 3.9 33.1 + - - +
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Residues in contact with GLU 40 (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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33A CYS* 4.1 6.2 - - - -
34A LEU 3.1 11.7 - - - +
35A ARG* 3.9 22.8 - - + -
38A GLU 4.3 0.2 + - - -
39A ARG* 1.3 77.1 - - - +
41A GLY* 1.3 59.9 - - - +
42A TRP* 2.9 32.7 + - + +
93A GLU* 4.0 14.6 - - - +
94A LEU* 3.7 7.5 - - - -
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Residues in contact with GLY 41 (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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33A CYS* 3.3 2.9 - - - -
34A LEU 2.8 34.3 + - - -
40A GLU* 1.3 75.1 - - - +
42A TRP* 1.3 65.6 + - - -
90A ALA* 3.5 25.6 - - - +
93A GLU* 3.6 11.7 - - - -
94A LEU* 4.0 3.2 - - - +
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Residues in contact with TRP 42 (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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7A TYR* 3.6 38.8 - + - -
31A TYR* 4.1 14.4 - + + -
32A VAL 3.2 15.5 - - - -
33A CYS* 3.6 22.1 - - + -
40A GLU* 2.9 28.8 + - + -
41A GLY* 1.3 82.4 - - - -
43A GLY* 1.3 59.3 + - - +
89A CYS 3.6 0.2 - - - -
90A ALA* 3.2 17.6 + - - +
93A GLU* 3.0 7.2 + - - +
269A LEU* 4.0 24.5 - - + -
273A GLN* 2.8 20.9 + - - -
300A VAL* 4.3 20.0 - - + -
301A ARG* 3.6 28.5 - - - +
313A VAL* 3.9 19.7 - - + -
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Residues in contact with GLY 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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31A TYR* 3.3 8.3 - - - +
32A VAL* 3.0 32.6 + - - +
42A TRP* 1.3 76.2 - - - +
44A GLU* 1.3 60.3 + - - -
45A ILE* 4.1 2.7 - - - -
86A GLY* 3.4 20.9 - - - -
89A CYS* 4.4 0.4 - - - -
90A ALA* 3.8 1.6 - - - +
269A LEU* 4.0 6.0 - - - +
273A GLN* 3.8 11.0 - - - -
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Residues in contact with GLU 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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9A TRP* 3.4 8.8 - - - -
30A LEU 3.5 8.1 - - - +
31A TYR* 3.5 7.8 - - + -
43A GLY* 1.3 72.8 - - - -
45A ILE* 1.3 62.4 + - - +
46A SER* 2.8 30.8 + - - +
82A SER 3.8 1.6 - - - +
85A PHE* 4.0 12.9 - - + -
86A GLY* 3.2 20.7 + - - -
237A THR* 5.0 1.6 + - - +
266A GLU* 3.4 16.7 - - + -
267A SER* 2.6 48.0 + - - -
269A LEU* 4.2 0.9 - - + -
270A GLY* 2.9 29.3 + - - +
273A GLN* 4.1 4.0 + - - +
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Residues in contact with ILE 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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29A GLY* 3.8 0.3 - - - -
30A LEU* 2.9 48.6 + - + +
32A VAL* 3.7 33.0 - - + +
43A GLY 4.0 4.5 - - - +
44A GLU* 1.3 80.4 - - - +
46A SER* 1.3 58.8 + - - +
47A PRO* 3.7 1.5 - - - +
59A ALA* 3.9 12.6 - - + +
63A LEU* 3.8 22.9 - - + -
82A SER* 3.6 32.1 - - - +
83A VAL* 3.8 27.4 - - + +
86A GLY* 3.8 9.9 - - - -
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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