Contacts of the strand formed by residues 43 - 52 (chain A) in PDB entry 2YU7
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 PHE 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A TYR* 4.2 17.7 - + - -
33A VAL* 4.5 17.5 - - + -
34A ARG 3.1 20.4 - - - +
35A GLU* 3.8 26.7 - - + -
36A SER* 3.8 2.1 - - - +
41A GLY* 4.0 13.9 - - - -
42A ASP* 1.3 84.6 - - - +
44A VAL* 1.3 69.7 + - - +
66A LYS* 4.2 1.2 - - - +
67A VAL* 2.9 40.2 + - + +
69A CYS* 4.0 9.9 - - + -
74A TYR* 3.5 40.8 - + - -
85A LEU* 4.6 5.2 - - + -
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Residues in contact with VAL 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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32A LEU 3.6 3.8 - - - +
33A VAL* 4.0 1.8 - - - -
34A ARG* 2.9 69.8 + - + +
36A SER* 4.3 8.7 - - - -
39A GLN* 6.2 1.6 - - + -
43A PHE* 1.3 82.1 - - - +
45A LEU* 1.3 63.4 + - - +
46A SER* 3.6 7.4 + - - +
64A HIS* 4.0 9.6 - - + -
65A ILE 4.1 3.1 - - - +
66A LYS* 5.2 0.9 - - + -
67A VAL* 4.1 2.2 - - - +
8B PTR 3.2 53.8 - - + +
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Residues in contact with LEU 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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31A PHE* 4.2 12.1 - - + -
32A LEU 4.1 4.5 - - - +
33A VAL* 3.7 31.4 - - + -
44A VAL* 1.3 71.1 - - - +
46A SER* 1.3 54.7 + - - +
47A VAL* 3.1 36.3 - - + -
63A THR 2.8 22.0 - - - +
64A HIS* 3.4 0.2 - - - -
65A ILE* 2.8 49.1 + - + +
67A VAL* 3.5 15.1 - - + +
76A VAL* 5.6 1.1 - - + -
85A LEU* 5.0 2.0 - - + -
88A LEU* 5.6 4.7 - - + -
89A VAL* 4.6 10.1 - - + -
92A PHE* 6.4 0.2 - - + -
97A ILE* 4.9 5.6 - - + -
107A LEU* 3.7 16.6 - - + -
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Residues in contact with SER 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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18A ALA* 3.8 11.4 - - - +
22A LEU* 3.7 20.9 - - - +
30A THR 3.6 1.2 - - - +
31A PHE* 3.2 1.7 - - - -
32A LEU* 2.8 42.7 + - - -
34A ARG* 3.4 26.2 + - - -
44A VAL* 3.6 1.9 + - - +
45A LEU* 1.3 71.3 - - - +
47A VAL* 1.3 62.7 + - - +
62A VAL* 4.0 1.8 - - - -
63A THR 3.3 4.7 - - - -
64A HIS* 3.5 18.2 + - - -
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Residues in contact with VAL 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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22A LEU* 4.3 0.4 - - - -
29A TRP* 4.3 0.7 - - + -
30A THR 3.1 13.5 - - - +
31A PHE* 3.7 13.5 - - + -
45A LEU* 3.1 32.5 - - + +
46A SER* 1.3 72.8 - - - +
48A LEU* 1.3 65.1 + - - +
49A SER 3.6 1.4 + - - -
62A VAL* 3.3 8.1 - - - +
63A THR* 2.9 36.3 + - - +
65A ILE* 4.6 3.8 - - + -
97A ILE* 5.5 0.2 - - + -
105A VAL* 3.1 36.3 - - + +
106A TYR 3.6 18.8 - - - +
107A LEU* 4.1 4.7 - - + -
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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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22A LEU* 3.4 34.0 - - + +
23A GLN* 3.8 14.6 - - + +
26A GLY* 4.5 1.6 - - - -
27A GLU 3.2 29.8 - - - +
29A TRP* 2.6 36.4 + - - -
30A THR* 2.7 17.2 + - - +
47A VAL* 1.3 72.0 - - - +
49A SER* 1.3 58.2 + - - +
60A LEU* 3.1 55.0 - - + +
61A ARG 3.9 0.2 - - - -
62A VAL* 3.5 16.6 - - + -
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Residues in contact with SER 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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29A TRP* 4.5 15.5 - - - -
47A VAL 3.6 2.2 + - - -
48A LEU* 1.3 73.4 - - - +
50A ASP* 1.3 58.3 + - - +
51A GLN* 3.0 24.7 + - - +
60A LEU* 2.9 30.6 - - - +
61A ARG* 2.8 30.4 + - - +
63A THR* 5.2 8.1 - - - -
105A VAL* 6.1 3.8 - - - +
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Residues in contact with ASP 50 (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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28A PRO* 3.5 33.4 - - + +
29A TRP* 4.1 29.2 + - + +
48A LEU 3.9 1.0 + - - -
49A SER* 1.3 71.3 - - - +
51A GLN* 1.3 69.1 + - + +
52A PRO* 3.9 6.3 - - - +
60A LEU* 4.3 9.4 - - - +
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Residues in contact with GLN 51 (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 TRP* 6.2 2.7 - - + -
49A SER* 3.0 14.8 + - - +
50A ASP* 1.3 91.3 + - + +
52A PRO* 1.3 77.9 - - - +
60A LEU* 3.8 2.4 - - - -
61A ARG* 3.2 23.3 + - + +
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Residues in contact with PRO 52 (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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50A ASP 3.9 7.4 - - - +
51A GLN* 1.3 99.9 - - + +
53A LYS* 1.3 64.9 + - - +
54A ALA* 3.5 2.9 + - - +
55A GLY* 3.5 36.1 - - - +
58A SER* 3.5 12.3 - - - +
59A PRO 3.8 7.2 - - - +
60A LEU* 4.2 11.2 - - + -
61A ARG* 5.2 0.6 - - - +
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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