Contacts of the strand formed by residues 38 - 45 (chain Q) in PDB entry 5C3I
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 38 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q VAL* 3.9 25.6 - - + -
28Q PHE* 3.9 29.6 - - + -
34Q LEU* 4.8 4.3 - - + -
36Q GLU 4.3 0.8 + - - +
37Q ASP* 1.3 75.0 - - - +
39Q GLU* 1.3 59.5 + - - +
40Q TRP* 4.0 20.3 + - + +
60Q VAL 3.8 0.5 - - - +
61Q LEU* 3.5 4.3 - - - -
62Q VAL* 2.9 38.8 + - + +
65Q VAL* 4.5 12.6 - - + -
99Q CYS* 4.0 2.7 - - - -
100Q THR 3.6 9.6 - - - +
101Q TYR* 3.8 24.7 - - + -
106Q PHE* 3.9 22.2 - - + -
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Residues in contact with GLU 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q ASP 4.0 1.3 + - - +
38Q LEU* 1.3 72.3 - - - +
40Q TRP* 1.3 62.5 + - - +
41Q LYS* 2.9 39.3 + - + +
59Q SER* 3.1 18.0 + - - +
60Q VAL 3.5 4.3 - - - +
61Q LEU* 3.8 22.7 - - + +
98Q THR* 3.7 0.9 + - - +
99Q CYS* 3.1 4.7 - - - -
100Q THR* 2.9 52.7 + - - +
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Residues in contact with TRP 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q VAL* 5.4 1.3 - - + -
6Q VAL* 3.5 32.8 - - + -
9Q VAL* 5.9 0.4 - - + -
26Q ILE* 3.6 36.8 - - + -
28Q PHE* 4.0 29.6 - + + -
38Q LEU* 4.0 17.4 - - + +
39Q GLU* 1.3 76.5 - - - +
41Q LYS* 1.3 60.0 + - - +
59Q SER* 3.4 3.1 + - - -
60Q VAL* 2.9 37.0 + - + +
62Q VAL* 4.0 19.5 - - + +
72Q PHE* 3.8 25.5 - + + -
74Q PHE* 3.3 21.9 - - + -
97Q ILE* 4.0 12.6 - - + -
98Q THR 3.3 10.1 - - - -
99Q CYS* 3.4 35.2 - - + -
107Q ILE* 5.3 1.1 - - + -
109Q VAL* 6.1 2.2 - - + -
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Residues in contact with LYS 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Q GLU* 2.9 34.9 + - + +
40Q TRP* 1.3 74.8 - - - +
42Q ILE* 1.3 64.3 + - - +
43Q ILE* 4.1 13.9 - - + -
56Q VAL* 4.4 20.7 - - + +
58Q ASP 3.5 5.8 - - - +
59Q SER* 3.6 22.3 + - - +
74Q PHE* 4.0 0.4 - - - -
96Q LEU 3.6 0.5 - - - +
97Q ILE* 3.4 6.6 - - - +
98Q THR* 2.9 48.5 + - - +
100Q THR* 5.6 8.1 - - + -
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Residues in contact with ILE 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q PHE* 5.0 2.2 - - + -
24Q PHE* 3.6 30.3 - - + -
41Q LYS* 1.3 72.8 - - - +
43Q ILE* 1.3 59.7 + - - +
56Q VAL* 3.5 2.6 - - - -
57Q LEU* 2.7 51.7 + - + +
58Q ASP 3.2 8.4 + - - +
74Q PHE* 3.5 49.8 - - + +
76Q ALA* 3.8 22.4 - - + +
95Q VAL* 4.0 18.8 - - + -
96Q LEU 3.3 7.0 - - - +
97Q ILE* 4.4 6.1 - - + -
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Residues in contact with ILE 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Q LYS* 4.5 13.9 - - + -
42Q ILE* 1.3 78.3 - - - +
44Q TYR* 1.3 64.0 + - - +
45Q VAL* 4.6 1.6 - - + +
54Q ASP* 4.0 26.7 - - + +
55Q GLN 3.4 7.4 - - - +
56Q VAL* 4.1 19.7 - - + +
94Q VAL 4.0 0.7 - - - +
95Q VAL* 3.3 8.1 - - - +
96Q LEU* 2.8 61.6 + - + +
98Q THR* 4.0 30.5 - - + +
108Q ARG* 5.3 5.4 - - - +
129R ARG* 5.8 0.4 - - - +
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Residues in contact with TYR 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q PHE* 3.9 11.7 - + - -
22Q PHE* 4.0 19.5 - + - -
43Q ILE* 1.3 71.4 - - - +
45Q VAL* 1.3 78.8 + - - +
46Q GLY* 3.0 12.1 + - - -
53Q TYR 4.0 0.2 - - - +
54Q ASP* 4.3 0.7 - - - -
55Q GLN* 2.7 45.1 + - + +
57Q LEU* 3.9 18.8 - - + +
79Q PRO* 3.7 33.0 - - + -
84Q ILE* 4.0 17.8 - - + +
89Q ALA 5.4 0.3 + - - -
93Q THR* 3.4 14.7 - - + +
94Q VAL 4.0 2.2 - - - -
95Q VAL* 3.8 21.8 - - + -
113Q VAL* 4.9 5.6 - - + -
115Q ASN* 3.1 27.4 + - - -
137Q ARG* 5.7 1.1 - - - -
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Residues in contact with VAL 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Q ILE* 4.8 1.3 - - + -
44Q TYR* 1.3 72.9 - - - +
46Q GLY* 1.3 61.7 + - - +
47Q SER 3.4 28.3 - - - +
48Q ALA* 4.0 6.7 - - - +
54Q ASP* 3.9 15.5 - - + +
93Q THR* 2.5 31.5 + - - +
94Q VAL* 3.1 41.9 + - + +
96Q LEU* 4.4 14.1 - - + -
126R LEU* 4.9 2.7 - - + -
129R ARG* 3.7 30.5 - - + +
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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