Contacts of the strand formed by residues 65 - 76 (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 GLY 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASN* 3.8 10.1 - - - -
61A ILE* 2.7 53.4 + - - +
64A TYR* 1.3 78.9 - - - +
66A LEU* 1.3 59.4 + - - -
196B HIS* 5.7 2.5 - - - -
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Residues in contact with LEU 66 (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* 3.1 44.4 - - + -
58A PHE* 3.6 21.1 - - + -
59A LYS 3.3 8.3 - - - +
60A ASN* 3.1 49.8 - - + +
65A GLY* 1.3 71.4 - - - -
67A VAL* 1.3 64.1 + - - +
68A ASP* 5.5 0.3 - - - +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A PHE* 3.2 6.9 - - - +
59A LYS* 2.9 41.3 + - + +
61A ILE* 4.3 12.1 - - + -
64A TYR* 4.1 20.0 - - + -
65A GLY 3.8 0.2 + - - -
66A LEU* 1.3 78.5 - - - +
68A ASP* 1.3 64.1 + - - +
87A TRP* 3.5 27.2 - - + -
61B ILE* 4.4 3.4 - - + -
64B TYR* 3.7 42.2 - - + +
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Residues in contact with ASP 68 (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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56A THR* 3.8 6.4 - - + +
57A SER 3.1 11.9 - - - +
58A PHE* 3.7 22.4 - - + -
66A LEU 5.5 0.2 - - - +
67A VAL* 1.3 80.1 - - - +
69A SER* 1.3 55.9 + - - +
70A ASN* 3.9 11.6 + - - +
87A TRP* 4.0 2.8 - - - -
228A TRP* 5.9 3.3 - - - -
263A HIS* 2.8 31.2 + - - +
264A GLY* 3.3 30.8 + - - +
64B TYR* 5.2 0.7 - - - -
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Residues in contact with SER 69 (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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55A HIS* 3.7 1.6 + - - +
56A THR* 3.2 5.5 - - - -
57A SER* 2.9 36.5 + - - -
68A ASP* 1.3 77.0 - - - +
70A ASN* 1.3 62.2 + - - +
87A TRP* 3.5 26.0 - - - -
120A ASP* 3.6 16.8 + - - +
121A ARG* 2.8 26.3 + - - -
262A GLY 3.4 7.0 - - - -
263A HIS* 4.1 4.3 - - - -
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Residues in contact with ASN 70 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.9 23.9 - - + +
55A HIS* 3.2 4.5 - - - -
56A THR* 2.9 28.2 + - - +
68A ASP* 3.9 3.8 - - - +
69A SER* 1.3 73.2 + - - +
71A GLY* 1.3 56.6 + - - +
84A ASP* 4.3 1.0 - - - +
85A THR 6.1 0.2 - - - -
121A ARG* 2.8 31.5 + - - -
218A PHE* 3.4 4.3 - - + -
260A VAL* 4.4 2.9 - - + +
261A PRO* 2.9 30.0 + - - +
262A GLY 2.9 7.3 + - - +
263A HIS 3.7 1.4 - - - +
264A GLY 2.8 38.0 + - - +
277A VAL* 5.9 0.2 - - - +
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.5 5.0 - - - +
55A HIS* 2.8 45.4 + - - +
70A ASN* 1.3 74.7 - - - +
72A LEU* 1.3 70.9 + - - +
83A ILE 3.1 14.8 - - - -
84A ASP* 4.2 2.0 - - - -
218A PHE* 4.0 7.2 - - - -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ILE* 4.0 15.3 - - + -
52A VAL* 4.2 7.2 - - + -
53A TYR 3.2 14.4 - - - +
54A LEU* 3.9 18.4 - - + -
55A HIS* 3.6 5.6 - - - -
71A GLY* 1.3 84.0 - - - +
73A VAL* 1.3 62.1 + - - +
74A VAL* 4.3 7.2 - - + -
82A ILE* 3.5 3.3 - - - -
83A ILE* 2.8 45.3 + - + +
205A LEU* 3.9 27.8 - - + -
216A ILE* 4.4 11.0 - - + -
218A PHE* 3.8 31.2 - - + -
260A VAL* 4.4 6.1 - - + -
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A VAL* 5.0 1.1 - - + -
51A GLY 3.8 0.2 - - - +
52A VAL* 3.5 4.0 - - - +
53A TYR* 3.0 45.0 + - + +
55A HIS* 4.0 8.1 - - + -
72A LEU* 1.3 74.3 - - - +
74A VAL* 1.3 66.3 + - - +
75A LEU* 4.2 6.1 - - + -
80A ALA* 4.1 22.7 - - + -
81A TYR 3.4 9.6 - - - +
82A ILE* 4.7 6.3 - - + -
95A LEU* 3.7 33.2 - - + -
98A TRP* 4.2 21.5 - - + -
99A ALA* 5.6 2.5 - - + -
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Residues in contact with VAL 74 (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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51A GLY 3.4 7.6 - - - +
52A VAL* 4.6 6.1 - - + -
72A LEU* 4.5 6.1 - - + -
73A VAL* 1.3 78.0 - - - +
75A LEU* 1.3 64.7 + - - +
79A GLN 3.8 0.7 - - - +
80A ALA* 3.5 2.4 - - - -
81A TYR* 2.8 41.4 + - - +
83A ILE* 4.0 20.9 - - + -
186A LEU* 3.5 36.6 - - + +
187A ILE* 4.4 8.1 - - + -
205A LEU* 3.7 32.8 - - + -
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Residues in contact with LEU 75 (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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51A GLY* 2.7 35.1 + - - +
53A TYR* 3.6 29.8 - - + +
73A VAL* 4.2 9.9 - - + -
74A VAL* 1.3 77.0 - - - +
76A ASP* 1.3 60.7 + - - +
77A ASN 4.1 8.7 - - - +
79A GLN 3.5 2.7 - - - +
80A ALA* 3.7 23.1 - - + -
98A TRP* 4.9 0.7 - - + -
106A TYR* 3.3 54.1 - - + +
186A LEU* 4.1 12.4 - - - +
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Residues in contact with ASP 76 (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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75A LEU* 1.3 74.2 - - - +
77A ASN* 1.3 81.2 + - - +
79A GLN* 2.9 41.0 + - + +
81A TYR* 4.7 5.8 + - + -
183A GLY* 5.2 6.8 - - - +
184A ASN* 5.4 5.4 + - - -
186A LEU* 4.2 23.1 - - + +
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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