Contacts of the strand formed by residues 39 - 49 (chain A) in PDB entry 2Y1T
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ILE* 4.3 3.3 - - - +
38A GLU* 1.3 79.0 - - - +
40A LYS* 1.3 65.5 + - - +
41A LEU* 3.8 24.9 - - + -
73A THR* 3.3 31.4 - - + -
93A PRO* 3.8 19.7 - - + -
94A ALA 3.2 29.6 - - - -
95A TYR* 4.3 2.2 - - + -
65C TYR* 3.7 42.0 - + + +
66C LYS* 5.9 7.6 - - + -
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Residues in contact with LYS 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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30A GLU* 4.3 10.9 + - - -
32A VAL* 3.5 28.0 - - + -
33A ALA 5.5 2.0 - - - +
34A ILE* 3.8 23.5 - - + +
39A PHE* 1.3 83.1 - - - +
41A LEU* 1.3 85.1 + - - +
42A VAL* 3.4 4.7 + - + +
43A PRO* 4.6 9.6 - - - -
94A ALA* 2.8 35.6 + - - +
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Residues in contact with LEU 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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39A PHE* 3.8 16.9 - - + -
40A LYS* 1.3 92.3 - - - +
42A VAL* 1.3 61.0 + - - +
43A PRO* 3.4 4.2 - - - +
91A PHE* 3.5 45.9 - - + -
92A PHE 3.8 1.1 - - - -
93A PRO* 4.0 26.5 - - + -
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Residues in contact with VAL 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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28A ALA* 3.8 15.7 - - + -
32A VAL* 4.2 27.4 - - + -
34A ILE* 4.5 0.2 - - + -
40A LYS* 3.9 4.9 - - + +
41A LEU* 1.3 67.8 - - - +
43A PRO* 1.3 80.9 - - + +
44A LEU* 3.6 1.2 + - - +
91A PHE* 3.3 2.2 - - - -
92A PHE* 2.8 47.3 + - + +
94A ALA* 3.9 20.2 - - + -
102A ILE* 4.2 13.9 - - + -
108A ILE* 3.2 30.7 - - + -
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Residues in contact with PRO 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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8A LEU* 6.0 2.7 - - + -
28A ALA* 3.5 6.4 - - - -
29A ALA* 2.8 37.0 + - + +
30A GLU* 3.9 33.0 - - + +
32A VAL* 4.3 11.7 - - + -
40A LYS* 4.6 2.7 - - - -
41A LEU 3.4 10.3 - - - +
42A VAL* 1.3 88.9 - - + +
44A LEU* 1.3 59.8 + - - +
45A GLY* 4.5 1.8 - - - +
90A TRP 3.9 0.4 - - - +
91A PHE* 3.7 24.9 - - + -
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Residues in contact with LEU 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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12A GLN* 4.3 3.5 - - - +
26A LEU* 4.1 14.7 - - + +
27A ARG* 3.1 34.3 + - - +
29A ALA* 4.1 1.1 - - - -
42A VAL 3.8 6.1 - - - +
43A PRO* 1.3 76.7 - - - +
45A GLY* 1.3 64.1 + - - +
46A VAL* 3.2 21.1 + - + +
58A VAL* 5.2 2.5 - - + -
90A TRP* 3.0 23.4 + - + +
91A PHE 3.6 28.3 - - - +
92A PHE* 3.9 3.4 - - + +
108A ILE* 3.3 41.5 - - + -
109A CYS* 3.8 23.6 - - - -
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Residues in contact with GLY 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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7A TYR* 3.4 5.5 - - - -
8A LEU* 2.8 41.2 + - - +
12A GLN* 3.9 9.7 - - - +
29A ALA* 3.7 18.7 - - - +
43A PRO* 3.5 4.0 - - - +
44A LEU* 1.3 79.7 - - - +
46A VAL* 1.3 61.0 + - - +
89A PHE* 3.9 7.4 - - - +
90A TRP 4.1 2.4 + - - -
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Residues in contact with VAL 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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5A ILE* 3.9 18.2 - - + -
6A LYS 3.6 3.4 - - - -
7A TYR* 3.7 28.0 - - + -
12A GLN* 6.0 0.4 - - + -
15A ILE* 4.9 8.5 - - + -
26A LEU* 4.3 13.7 - - + -
44A LEU* 3.2 15.5 - - + +
45A GLY* 1.3 85.3 - - - +
47A ALA* 1.3 56.8 - - - +
48A MET* 3.8 21.1 - - + -
89A PHE* 3.3 7.0 - - - -
90A TRP* 2.7 47.4 + - + -
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Residues in contact with ALA 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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5A ILE* 3.4 3.6 - - - +
6A LYS* 2.9 39.2 + - + +
46A VAL* 1.3 72.3 - - - +
48A MET* 1.3 62.8 + - - +
85A GLY 4.1 5.6 - - - +
88A ASP* 3.4 27.6 - - + +
89A PHE* 3.6 15.7 - - + -
90A TRP* 4.3 1.6 - - - -
128B LEU* 3.6 20.6 - - + +
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Residues in contact with MET 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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3A ILE* 3.8 21.8 - - + -
4A LYS 3.1 9.0 - - - +
5A ILE* 4.0 24.0 - - + -
15A ILE* 5.1 0.7 - - - -
26A LEU* 4.3 3.6 - - + -
46A VAL* 3.8 23.1 - - + -
47A ALA* 1.3 80.7 - - - +
49A GLU* 1.3 61.4 + - - +
50A LEU* 4.0 8.2 + - + +
79A ILE* 5.9 0.2 - - - +
83A TYR 3.2 22.7 - - - +
84A LYS* 3.5 4.5 - - - +
88A ASP 4.4 1.0 + - - -
90A TRP* 3.6 49.7 + - + +
111A PHE* 3.8 29.6 - - + -
122B LEU* 5.3 0.7 - - - -
128B LEU* 3.8 6.5 - - - +
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Residues in contact with GLU 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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2A GLN 4.2 1.4 - - - +
3A ILE* 3.6 5.8 - - - -
4A LYS* 2.8 67.9 + - + +
48A MET* 1.3 71.7 - - - +
50A LEU* 1.3 72.7 + - - +
84A LYS* 3.9 43.7 + - + +
128B LEU* 4.1 16.1 - - + +
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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