Contacts of the strand formed by residues 34 - 39 (chain A) in PDB entry 2YSX
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 SER 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.8 13.0 - - - -
29A THR* 3.3 33.6 - - - +
31A LYS* 3.6 15.7 + - - +
33A GLY* 1.3 78.6 - - - +
35A PHE* 1.3 64.9 + - - +
51A VAL* 3.7 4.9 - - - +
52A LEU* 3.2 29.5 + - - +
102A THR* 4.6 0.2 - - - +
106A TYR* 3.8 8.4 + - - +
108A VAL* 3.2 17.1 - - - +
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Residues in contact with PHE 35 (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 TRP* 3.6 22.7 - + + +
26A LEU* 4.2 1.6 - - - -
33A GLY 4.4 0.2 - - - -
34A SER* 1.3 78.1 - - - +
36A LEU* 1.3 66.1 - - - +
49A LEU* 4.1 10.8 - - + -
50A CYS 3.2 12.6 - - - +
51A VAL* 4.2 3.4 - - + -
90A ILE* 3.4 24.0 - - + -
94A LYS* 3.3 30.7 - - - -
104A LEU* 3.3 44.4 - - + -
106A TYR 3.6 9.9 - - - -
107A PRO* 3.3 35.1 - - + +
108A VAL* 3.1 28.8 + - - +
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Residues in contact with LEU 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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12A TRP 3.6 6.5 - - - -
14A HIS* 3.7 13.9 - - + -
17A ILE* 4.7 6.3 - - + -
22A ALA* 3.3 34.1 - - + +
25A LEU* 4.0 13.2 - - + -
26A LEU* 3.7 18.4 - - + -
35A PHE* 1.3 81.3 - - - +
37A VAL* 1.3 78.5 + - - +
38A ARG* 4.8 2.0 - - + +
49A LEU* 3.1 8.0 - - - +
50A CYS* 2.9 52.8 + - + +
108A VAL* 3.6 20.9 - - + -
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Residues in contact with VAL 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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12A TRP* 2.7 45.5 + - + +
13A ASN* 4.4 7.0 - - - +
14A HIS* 3.3 28.3 + - - +
15A GLY 3.7 0.4 + - - -
35A PHE* 5.1 0.7 - - + -
36A LEU* 1.3 83.9 - - - +
38A ARG* 1.3 73.7 + - - +
47A TYR* 4.0 31.0 - - + -
48A ALA 3.3 11.2 - - - +
49A LEU* 4.1 8.7 - - + -
62A ILE* 5.7 0.9 - - + -
86A LEU* 4.7 10.1 - - + -
90A ILE* 3.8 18.8 - - + -
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Residues in contact with ARG 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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13A ASN* 6.0 0.2 - - - -
15A GLY* 3.1 18.6 - - - +
17A ILE* 3.3 43.7 + - + -
18A THR 4.5 2.9 - - - -
19A ARG* 5.0 14.8 - - - +
22A ALA* 4.4 10.1 - - - +
36A LEU* 4.8 3.1 - - + -
37A VAL* 1.3 79.3 - - - +
39A ALA* 1.3 65.8 + - - +
40A SER* 5.0 6.1 + - - +
41A GLU* 4.3 16.5 + - - +
47A TYR* 3.6 11.0 - - - -
48A ALA* 2.8 63.3 + - + +
50A CYS* 3.7 13.9 - - - -
59A THR* 3.5 21.6 - - - +
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Residues in contact with ALA 39 (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* 2.9 11.4 + - - -
16A ASN* 3.9 27.9 - - + +
17A ILE 4.5 3.6 + - - +
38A ARG* 1.3 79.5 + - - +
40A SER* 1.3 68.5 + - - +
41A GLU* 3.2 7.3 + - - +
44A SER* 5.2 8.7 - - - +
46A ALA 4.4 2.5 - - - +
47A TYR* 4.3 15.2 - - + -
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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