Contacts of the strand formed by residues 25 - 32 (chain A) in PDB entry 6LU7
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 THR 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A THR* 3.2 5.5 - - - +
22A CYS 2.9 31.0 + - - -
23A GLY 3.4 0.2 - - - -
24A THR* 1.3 82.2 + - - +
26A THR* 1.3 63.0 + - - +
27A LEU* 4.8 5.2 - - + -
41A HIS* 4.1 4.9 - - + +
42A VAL* 3.3 41.3 + - + +
44A CYS 2.7 23.7 + - - +
45A THR* 4.5 4.2 - - - -
49A MET* 5.2 7.2 - - + +
6C 010 3.7 21.2 - - + -
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Residues in contact with THR 26 (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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19A GLN* 3.5 29.9 + - - +
20A VAL 3.4 4.3 - - - -
21A THR* 3.8 12.8 - - - -
24A THR 4.5 3.8 - - - +
25A THR* 1.3 73.6 - - - +
27A LEU* 1.3 63.1 + - - +
119A ASN* 3.7 16.6 + - - +
143A GLY* 4.5 6.4 - - - -
6C 010 2.9 40.3 - - + -
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Residues in contact with LEU 27 (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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19A GLN* 3.5 7.1 - - - +
20A VAL* 2.8 35.1 + - + -
25A THR* 4.8 4.3 - - + -
26A THR* 1.3 76.5 + - - +
28A ASN* 1.3 78.0 + - - +
38A CYS* 3.7 12.1 - - + -
39A PRO* 3.7 18.4 - - + -
41A HIS* 3.7 31.9 - - + +
42A VAL* 3.6 36.8 - - + +
119A ASN* 5.5 2.5 - - - +
120A GLY 5.3 0.7 - - - -
143A GLY 4.5 7.2 - - - +
145A CYS* 3.5 21.5 - - + +
5C PJE 4.9 5.2 - - + +
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Residues in contact with ASN 28 (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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17A MET* 3.9 17.5 - - + -
18A VAL 3.3 4.9 - - - +
20A VAL* 4.5 0.7 - - - -
27A LEU* 1.3 87.0 - - - +
29A GLY* 1.3 59.0 + - - +
38A CYS* 3.6 4.3 - - - +
117A CYS* 3.0 29.2 + - - +
119A ASN 3.4 3.8 + - - -
120A GLY* 2.7 32.6 + - - -
143A GLY 3.0 22.4 + - - -
144A SER 3.6 4.8 + - - -
145A CYS 2.9 27.2 + - - +
146A GLY* 3.2 22.1 - - - -
147A SER* 4.3 0.4 + - - -
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Residues in contact with GLY 29 (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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17A MET* 3.4 13.4 - - - +
18A VAL* 2.7 48.6 + - - -
20A VAL* 3.9 11.5 - - - +
28A ASN* 1.3 75.4 - - - +
30A LEU* 1.3 61.2 + - - -
36A VAL* 4.2 0.9 - - - -
37A TYR 3.1 11.0 - - - -
38A CYS* 4.1 0.4 - - - -
146A GLY 5.0 1.8 - - - -
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Residues in contact with LEU 30 (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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13A VAL* 4.8 0.9 - - + -
16A CYS* 3.6 17.9 - - + -
17A MET* 3.8 22.7 - - - -
29A GLY* 1.3 70.7 - - - -
31A TRP* 1.3 58.9 + - - +
32A LEU* 3.5 27.8 + - + -
36A VAL* 3.3 3.6 - - - -
37A TYR* 2.7 52.8 + - + +
103A PHE* 4.6 0.4 - - + -
148A VAL* 4.0 17.0 - - + -
159A PHE* 3.8 37.2 - - + -
162A MET* 4.4 1.8 - - + +
177A LEU* 3.8 22.4 - - + -
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Residues in contact with TRP 31 (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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15A GLY 5.2 2.0 - - - -
16A CYS* 2.6 27.1 + - - +
18A VAL* 3.7 26.9 - - + -
29A GLY 3.9 0.6 + - - -
30A LEU* 1.3 69.1 - - - +
32A LEU* 1.3 61.4 + - - +
33A ASP 2.9 22.3 + - - -
35A VAL 3.6 9.9 - - - -
36A VAL* 3.8 15.9 - - + -
70A ALA* 3.6 20.9 - - + -
75A LEU* 3.6 28.5 - - + -
91A VAL* 3.7 6.7 - - + +
93A THR* 3.2 33.2 + - + -
94A ALA 3.8 2.0 - - - -
95A ASN* 2.8 62.4 + - + +
96A PRO* 4.4 8.3 - - + -
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Residues in contact with LEU 32 (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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16A CYS* 3.8 23.6 - - + -
30A LEU* 3.5 16.3 + - + -
31A TRP* 1.3 79.7 - - - +
33A ASP* 1.3 72.4 + - - +
35A VAL* 3.0 26.4 + - - +
37A TYR* 4.2 9.4 + - + -
98A THR* 4.0 2.9 - - + -
99A PRO* 4.3 7.2 - - + -
101A TYR* 3.7 52.2 + - + +
103A PHE* 3.7 17.3 - - + -
159A PHE* 3.7 24.2 - - + -
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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