Contacts of the strand formed by residues 35 - 41 (chain A) in PDB entry 4Q29
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 GLY 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.1 1.1 - - - -
25A LEU* 4.2 15.7 - - - -
34A PHE* 1.3 79.2 - - - +
36A GLY* 1.3 58.5 + - - -
105A ILE* 3.3 10.9 - - - +
106A TRP* 2.9 51.5 + - - +
111A SER* 5.5 0.8 - - - -
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Residues in contact with GLY 36 (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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23A ARG* 3.5 3.5 - - - +
24A LEU* 2.9 30.3 + - - +
25A LEU* 4.7 1.1 + - - +
34A PHE* 6.1 0.2 - - - -
35A GLY* 1.3 75.8 - - - -
37A ALA* 1.3 64.4 + - - +
103A TYR* 4.0 10.1 - - - -
104A THR 2.9 14.1 - - - -
105A ILE* 4.2 0.9 - - - -
106A TRP* 3.6 19.3 - - - -
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Residues in contact with ALA 37 (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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21A GLY* 5.2 1.8 - - - -
22A SER 3.3 15.5 - - - +
23A ARG* 4.0 15.9 - - + +
36A GLY* 1.3 76.9 - - - +
38A TRP* 1.3 64.0 + - - +
39A CYS* 3.7 10.1 + - - -
103A TYR* 3.3 12.6 - - - -
104A THR* 2.9 46.0 + - + +
106A TRP* 4.2 5.6 - - + -
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Residues in contact with TRP 38 (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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8A MSE 3.9 21.5 - - + -
10A TRP* 3.6 17.0 - + - -
13A MSE 3.6 19.5 - - + +
21A GLY* 3.2 4.3 - - - -
22A SER* 2.8 38.2 + - - +
37A ALA* 1.3 72.7 - - - +
39A CYS* 1.3 69.8 + - - +
40A ILE* 4.1 0.4 - - + -
61A ILE* 3.7 39.7 - - + -
101A HIS* 3.0 29.7 + - - +
102A PHE 3.8 2.2 - - - -
103A TYR* 3.4 20.0 - + + -
59B ILE* 3.7 27.6 - - + -
60B VAL 3.3 28.7 - - - -
61B ILE* 4.4 0.2 - - - -
78B LYS* 4.1 7.6 - - + -
79B GLY* 3.5 22.7 - - - -
81B LEU* 5.2 1.1 - - + -
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Residues in contact with CYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.6 25.1 - - + -
20A ASP 3.3 3.6 - - - -
21A GLY* 5.0 0.7 - - - -
37A ALA* 3.8 9.2 - - - -
38A TRP* 1.3 79.3 - - - +
40A ILE* 1.3 66.9 + - - +
41A VAL 4.2 0.2 - - - -
100A PHE 3.7 0.3 - - - +
101A HIS* 3.3 4.9 - - - -
102A PHE* 2.8 65.6 + - + +
104A THR* 3.8 29.6 - - - -
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Residues in contact with ILE 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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10A TRP* 3.9 9.2 - - + -
13A MSE 3.4 37.2 - - + -
19A LEU* 3.4 4.7 - - - +
20A ASP* 2.8 36.8 + - + +
38A TRP* 4.1 0.4 - - + -
39A CYS* 1.3 78.7 - - - +
41A VAL* 1.3 66.5 - - - +
42A ARG* 3.7 42.8 + - - +
99A ASP* 3.8 22.2 - - + +
100A PHE 3.2 9.6 - - - +
101A HIS* 3.6 29.6 - - + +
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Residues in contact with VAL 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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18A ASP 5.2 2.5 - - - +
19A LEU* 4.3 15.7 - - + +
40A ILE* 1.3 75.0 - - - +
42A ARG* 1.3 60.9 + - - +
45A THR* 3.5 34.8 - - - +
46A LYS* 4.2 6.3 - - - -
47A SER* 4.7 1.8 - - - -
92A VAL* 3.7 36.8 - - + +
94A ASN* 3.0 33.3 + - + +
99A ASP* 3.9 0.3 - - - -
100A PHE* 2.8 27.2 + - + +
102A PHE* 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