Contacts of the strand formed by residues 52 - 61 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.8 0.5 - - - -
48A ILE* 2.9 32.1 + - + +
49A GLU* 3.1 11.1 + - + +
50A ASP 3.1 11.5 - - - +
51A GLY* 1.3 83.5 - - - +
53A TYR* 1.3 67.8 + - - +
72A LEU* 4.2 14.8 - - + -
73A VAL 3.5 6.7 - - - +
74A VAL* 4.6 5.8 - - + -
205A LEU* 4.2 18.6 - - + -
211A SER* 3.6 28.0 - - - +
216A ILE* 3.7 22.2 - - + -
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Residues in contact with TYR 53 (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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44A VAL* 3.9 16.4 - - + -
45A ILE* 3.3 6.7 - - - +
47A LYS* 3.6 50.6 + - + +
48A ILE* 4.5 0.9 - - - -
51A GLY* 4.3 3.5 + - - -
52A VAL* 1.3 87.0 - - - +
54A LEU* 1.3 60.9 + - - +
72A LEU* 3.2 11.4 - - - +
73A VAL* 3.0 44.9 + - + +
75A LEU* 3.6 30.9 - - + +
98A TRP* 3.5 33.9 - + - -
104A ARG* 5.8 1.8 + - - -
106A TYR* 5.2 2.8 + + - -
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Residues in contact with LEU 54 (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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43A GLU 3.7 1.0 - - - +
44A VAL* 3.3 2.8 - - - -
45A ILE* 2.7 56.5 + - + +
48A ILE* 3.8 21.0 - - + +
53A TYR* 1.3 72.6 - - - +
55A HIS* 1.3 59.0 + - - +
56A THR* 3.9 18.6 + - - +
70A ASN* 3.9 17.3 - - + +
71A GLY 3.5 15.0 - - - +
72A LEU* 3.9 5.4 - - + -
260A VAL* 3.8 27.1 - - + -
277A VAL* 4.3 20.2 - - + -
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Residues in contact with HIS 55 (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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42A LEU* 4.3 6.4 - - + +
43A GLU 3.2 8.3 - - - +
44A VAL* 4.1 5.8 - - + -
53A TYR 3.7 1.8 + - - -
54A LEU* 1.3 72.2 - - - +
56A THR* 1.3 62.9 + - - +
57A SER* 5.2 1.6 + - - -
69A SER 5.2 0.6 + - - -
70A ASN* 3.2 6.0 - - - +
71A GLY* 2.8 70.5 + - - +
72A LEU 3.4 17.1 + - - -
73A VAL* 4.0 5.4 - - + -
82A ILE* 4.0 0.2 - - - +
83A ILE 3.5 2.4 + - - -
84A ASP 2.8 29.4 + - - -
85A THR 3.9 2.5 - - - -
86A PRO* 3.7 30.2 - - + +
95A LEU* 3.8 33.5 - - + +
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Residues in contact with THR 56 (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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42A LEU* 3.5 4.1 - - - -
43A GLU* 2.8 44.8 + - - -
45A ILE* 5.8 0.7 - - - +
54A LEU* 3.9 15.1 + - - +
55A HIS* 1.3 73.2 - - - +
57A SER* 1.3 62.5 + - - +
58A PHE* 3.6 27.3 - - + -
68A ASP* 3.8 19.7 - - + +
69A SER 3.2 10.1 - - - +
70A ASN* 2.9 20.8 + - - +
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Residues in contact with SER 57 (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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42A LEU* 4.0 13.7 - - - +
55A HIS* 4.3 1.1 + - - -
56A THR* 1.3 74.5 - - - +
58A PHE* 1.3 65.9 + - - +
68A ASP* 3.1 7.3 - - - +
69A SER* 2.9 36.4 + - - -
86A PRO* 3.5 8.4 - - - +
87A TRP* 3.0 37.6 + - - +
91A ASP* 3.7 19.3 - - - -
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Residues in contact with PHE 58 (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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40A LYS* 3.6 50.4 + - + +
41A PRO 3.7 9.0 - - - -
43A GLU* 3.5 26.7 - - - -
56A THR* 3.6 30.5 - - + -
57A SER* 1.3 76.4 - - - +
59A LYS* 1.3 69.0 + - - +
66A LEU* 3.6 28.5 - - + -
67A VAL 3.2 7.0 - - - +
68A ASP* 3.7 27.1 - - + +
87A TRP* 4.6 3.9 - - - +
91A ASP* 4.5 9.5 + - - +
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Residues in contact with LYS 59 (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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58A PHE* 1.3 77.1 + - - +
60A ASN* 1.3 60.1 + - - +
61A ILE* 3.6 14.3 + - + -
65A GLY 3.5 2.4 - - - +
66A LEU* 3.3 7.1 - - - -
67A VAL* 2.9 47.5 + - + +
87A TRP* 3.2 65.1 + - + +
88A SER* 4.5 8.7 - - - -
61B ILE* 5.9 1.6 - - + -
62B GLU 4.7 4.9 - - - +
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Residues in contact with ASN 60 (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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58A PHE 4.4 0.2 - - - -
59A LYS* 1.3 70.9 - - - +
61A ILE* 1.3 68.7 + - - +
62A GLU* 3.6 4.5 + - - +
65A GLY* 3.8 11.4 - - - +
66A LEU* 3.1 26.7 - - + +
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Residues in contact with ILE 61 (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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59A LYS* 4.2 22.9 - - + +
60A ASN* 1.3 74.5 + - - +
62A GLU* 1.3 72.1 + - - +
63A GLY 3.0 0.5 + - - -
64A TYR* 2.9 26.3 + - + -
65A GLY* 2.7 48.7 + - - +
67A VAL* 4.3 6.5 - - + -
59B LYS* 6.0 2.0 - - + -
61B ILE* 3.0 56.1 - - + -
67B VAL* 5.0 4.0 - - + -
87B TRP* 4.7 7.2 - - + -
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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