Contacts of the strand formed by residues 52 - 61 (chain B) in PDB entry 2YNU
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 VAL 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B LYS* 3.7 1.9 - - - -
48B ILE* 2.9 46.0 + - + -
49B GLU* 3.2 20.0 + - + +
50B ASP 4.1 8.3 - - - +
51B GLY* 1.3 83.7 - - - +
53B TYR* 1.3 74.0 + - - +
72B LEU* 4.5 7.4 - - + -
73B VAL 3.6 4.9 - - - +
74B VAL* 4.3 7.4 - - + -
205B LEU* 4.2 19.1 - - + -
210B LYS* 5.9 0.2 - - - +
211B SER* 3.8 26.5 - - - +
216B ILE* 4.1 7.9 - - + -
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Residues in contact with TYR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 3.8 17.0 - - + -
45B ILE* 3.4 3.4 - - - -
47B LYS* 3.8 39.6 - - + +
48B ILE* 4.6 0.2 - - - -
51B GLY* 4.3 4.5 - - - -
52B VAL* 1.3 88.6 - - - +
54B LEU* 1.3 59.8 + - - +
72B LEU* 3.1 14.6 - - - +
73B VAL* 2.9 48.4 + - + +
75B LEU* 4.0 23.6 - - + +
98B TRP* 3.4 40.2 - + - -
104B ARG* 6.0 0.2 - - - -
106B TYR* 4.2 11.6 + - - -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLU 3.6 1.6 - - - +
44B VAL* 3.2 4.1 - - - -
45B ILE* 2.8 57.0 + - + +
48B ILE* 3.6 23.8 - - + +
53B TYR* 1.3 72.1 - - - +
55B HIS* 1.3 58.7 + - - +
56B THR* 3.9 18.5 + - - +
70B ASN* 4.0 15.5 - - + +
71B GLY 3.5 15.3 - - - +
72B LEU* 3.8 5.4 - - + -
260B VAL* 3.7 27.6 - - + -
277B VAL* 4.0 21.5 - - + -
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Residues in contact with HIS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 4.1 7.1 - - + +
43B GLU 3.2 7.4 - - - +
44B VAL* 4.2 6.1 - - + -
53B TYR 3.9 0.4 + - - -
54B LEU* 1.3 73.7 - - - +
56B THR* 1.3 61.4 + - - +
57B SER* 5.3 0.6 + - - -
69B SER 3.8 1.7 + - - +
70B ASN* 3.5 3.9 - - - +
71B GLY* 2.9 68.9 + - - +
72B LEU 3.3 19.9 + - - -
73B VAL* 4.2 3.1 - - + -
84B ASP 2.8 29.4 + - - -
85B THR 3.9 3.4 - - - -
86B PRO* 3.7 30.1 - - + +
95B LEU* 3.7 34.9 - - + +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 3.4 6.4 - - - +
43B GLU* 2.7 42.2 + - - -
45B ILE* 5.6 1.0 - - - +
54B LEU* 3.9 15.2 + - - +
55B HIS* 1.3 73.6 - - - +
57B SER* 1.3 64.2 + - - +
58B PHE* 3.2 37.9 - - + -
68B ASP* 4.0 12.6 - - + -
69B SER 3.6 3.1 - - - +
70B ASN* 3.0 23.2 + - - +
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 4.5 2.9 - - - +
55B HIS* 5.4 1.1 - - - -
56B THR* 1.3 74.1 - - - +
58B PHE* 1.3 64.6 + - - +
68B ASP* 3.3 5.2 - - - -
69B SER* 3.0 37.1 + - - -
86B PRO* 3.7 14.8 - - - +
87B TRP* 3.3 39.6 + - - +
88B SER* 4.5 0.5 + - - -
91B ASP* 3.0 23.5 + - - +
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Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LYS* 3.5 58.2 + - + +
41B PRO 3.8 15.0 - - - -
43B GLU* 3.8 22.2 - - - -
56B THR* 3.2 36.3 - - + -
57B SER* 1.3 81.1 + - - +
59B LYS* 1.3 74.0 + - - +
66B LEU* 4.0 26.5 - - + -
67B VAL 3.4 11.7 - - - +
68B ASP* 3.7 11.7 - - + -
87B TRP* 4.8 2.2 - - - -
91B ASP* 4.3 7.0 + - - +
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 6.0 1.8 - - + -
62A GLU 5.7 0.4 - - - +
58B PHE* 1.3 78.0 + - - +
60B ASN* 1.3 60.8 + - - +
61B ILE* 3.7 8.8 + - + -
66B LEU* 3.6 4.4 - - - -
67B VAL* 3.0 49.6 + - + +
87B TRP* 3.5 60.9 + - + +
88B SER* 4.0 18.2 - - - -
119B GLU* 6.0 0.2 - - - -
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Residues in contact with ASN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A TYR* 4.3 15.9 + - - -
59B LYS* 1.3 71.8 - - - +
61B ILE* 1.3 63.3 + - - +
62B GLU* 3.7 8.9 + - - +
65B GLY* 3.7 8.8 - - - -
66B LEU* 3.6 31.0 + - + -
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LYS* 6.1 1.6 - - + -
61A ILE* 3.0 57.9 - - + -
67A VAL* 4.4 5.2 - - + -
87A TRP* 5.0 3.1 - - + -
59B LYS* 3.7 8.0 + - + +
60B ASN* 1.3 74.5 + - - +
62B GLU* 1.3 68.4 + - - +
64B TYR* 3.0 43.8 + - + -
65B GLY* 3.1 21.3 + - - +
67B VAL* 4.4 15.5 - - + -
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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