Contacts of the strand formed by residues 65 - 76 (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 GLY 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A TYR* 3.2 26.4 - - - -
60B ASN* 3.7 13.5 - - - -
61B ILE* 3.1 27.8 + - - +
63B GLY 4.7 0.2 - - - +
64B TYR* 1.3 82.1 - - - +
66B LEU* 1.3 66.8 + - - +
67B VAL 3.6 1.0 + - - -
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Residues in contact with LEU 66 (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* 3.1 33.1 + - + +
40B LYS* 3.6 41.5 - - + +
58B PHE* 4.0 23.8 - - + -
59B LYS 3.6 22.2 - - - +
60B ASN* 3.6 16.3 + - + +
64B TYR* 5.2 1.7 - - - -
65B GLY* 1.3 71.5 - - - -
67B VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 67 (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* 5.0 4.3 - - + -
64A TYR* 3.9 31.6 - - + +
58B PHE* 3.4 8.3 - - - -
59B LYS* 3.0 48.1 + - + +
61B ILE* 4.4 15.5 - - + -
64B TYR* 3.9 27.8 - - + -
65B GLY 4.0 3.8 - - - +
66B LEU* 1.3 79.9 - - - +
68B ASP* 1.3 63.5 + - - +
87B TRP* 4.0 19.3 - - + -
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Residues in contact with ASP 68 (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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64A TYR* 4.5 2.8 - - - -
56B THR* 4.0 6.6 - - + +
57B SER 3.3 5.4 - - - +
58B PHE* 3.7 24.2 - - + -
67B VAL* 1.3 77.9 - - - +
69B SER* 1.3 55.3 + - - +
70B ASN* 4.0 6.1 - - - +
87B TRP* 3.6 4.9 - - - -
228B TRP* 4.5 9.2 - - - -
263B HIS* 2.7 31.7 + - - +
264B GLY* 2.6 40.0 + - - +
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Residues in contact with SER 69 (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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55B HIS* 3.8 1.9 + - - +
56B THR* 3.6 1.9 - - - -
57B SER* 3.0 33.8 + - - -
68B ASP* 1.3 73.5 - - - +
70B ASN* 1.3 63.5 + - - +
85B THR 5.4 0.5 + - - -
87B TRP* 3.3 34.0 + - - -
120B ASP* 3.5 15.3 + - - +
121B ARG* 3.1 22.7 + - - -
262B GLY 3.1 5.8 - - - -
263B HIS* 3.9 4.9 - - - -
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Residues in contact with ASN 70 (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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54B LEU* 4.0 23.0 - - + +
55B HIS* 3.5 3.8 - - - -
56B THR* 3.0 26.4 + - - +
68B ASP* 4.0 4.3 - - - +
69B SER* 1.3 76.7 - - - +
71B GLY* 1.3 57.8 + - - +
84B ASP* 5.2 0.2 - - - -
85B THR 6.1 0.2 - - - -
121B ARG* 3.0 27.7 + - - -
218B PHE* 3.4 7.2 - - - -
260B VAL* 4.2 4.7 - - + +
261B PRO* 3.0 30.5 + - - +
262B GLY 2.5 13.1 + - - +
264B GLY 2.8 37.0 + - - +
277B VAL* 5.5 0.6 - - - +
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Residues in contact with GLY 71 (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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54B LEU* 3.5 5.2 - - - +
55B HIS* 2.9 48.8 + - - +
70B ASN* 1.3 73.9 - - - +
72B LEU* 1.3 73.2 + - - +
83B ILE 3.2 10.8 - - - -
84B ASP* 4.2 2.5 - - - -
218B PHE* 4.0 5.4 - - - -
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Residues in contact with LEU 72 (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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48B ILE* 3.9 15.7 - - + -
52B VAL* 4.5 5.4 - - + -
53B TYR 3.1 15.3 - - - +
54B LEU* 3.8 17.5 - - + -
55B HIS* 3.4 10.6 - - - -
71B GLY* 1.3 81.7 - - - +
73B VAL* 1.3 66.1 + - - +
74B VAL* 4.2 1.3 - - + -
82B ILE* 3.5 4.2 - - - -
83B ILE* 2.8 48.3 + - + -
205B LEU* 4.0 27.4 - - + -
216B ILE* 4.6 8.5 - - + -
218B PHE* 3.9 30.7 - - + -
260B VAL* 4.3 6.7 - - + -
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Residues in contact with VAL 73 (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* 5.3 0.9 - - + -
51B GLY 3.7 1.7 - - - +
52B VAL* 3.6 3.5 - - - -
53B TYR* 2.9 48.0 + - + +
55B HIS* 4.2 5.8 - - + -
72B LEU* 1.3 78.6 - - - +
74B VAL* 1.3 62.7 + - - +
75B LEU* 4.7 4.9 - - + -
80B ALA* 3.8 28.0 - - + -
81B TYR 3.3 7.9 - - - +
82B ILE* 4.5 6.7 - - + -
95B LEU* 4.0 31.4 - - + -
98B TRP* 4.3 20.2 - - + -
99B ALA* 5.7 2.5 - - + -
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Residues in contact with VAL 74 (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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51B GLY 3.5 7.2 - - - +
52B VAL* 4.3 7.2 - - + +
72B LEU* 4.5 5.2 - - + -
73B VAL* 1.3 74.4 - - - +
75B LEU* 1.3 67.7 + - - +
79B GLN 3.6 0.7 - - - +
80B ALA* 3.5 1.6 - - - -
81B TYR* 2.8 44.6 + - - +
83B ILE* 3.9 18.8 - - + -
186B LEU* 4.0 25.4 - - + -
187B ILE* 4.1 10.1 - - + -
205B LEU* 3.8 44.0 - - + -
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Residues in contact with LEU 75 (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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51B GLY* 2.7 33.5 + - - +
53B TYR* 4.0 24.2 - - + +
73B VAL* 4.7 4.3 - - + -
74B VAL* 1.3 76.6 - - - +
76B ASP* 1.3 59.1 + - - +
77B ASN 3.8 20.3 + - - +
79B GLN 3.3 13.2 - - - +
80B ALA* 3.7 21.5 - - + -
106B TYR* 3.9 38.6 - - + +
186B LEU* 3.7 16.6 - - - +
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Residues in contact with ASP 76 (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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74B VAL 4.1 0.2 + - - -
75B LEU* 1.3 72.7 - - - +
77B ASN* 1.3 73.1 + - - +
79B GLN* 2.8 59.9 + - + +
81B TYR* 4.2 6.7 - - + -
183B GLY 4.3 11.9 - - - +
184B ASN* 5.4 3.4 - - - +
186B LEU* 4.0 24.8 - - + +
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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