Contacts of the strand formed by residues 61 - 68 (chain A) in PDB entry 1YDY
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 TYR 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.9 28.7 - - + -
33A VAL 3.3 2.4 + - - -
34A ILE* 3.4 8.6 - - + -
35A ALA 2.8 26.5 + - - -
59A ALA* 3.3 2.3 - - - +
60A ASP* 1.3 90.3 - - + +
62A LEU* 1.3 68.0 + - - +
63A GLU 4.1 0.2 - - - -
166A ILE* 4.3 0.2 - - - -
167A GLY* 3.3 14.8 - - - -
168A ILE 3.5 19.3 - - - -
169A TYR* 4.1 23.1 - + + -
204A LYS* 3.4 64.9 + - + +
205A VAL 4.6 0.3 + - - -
206A TYR* 3.6 28.3 + + - -
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Residues in contact with LEU 62 (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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35A ALA* 4.3 3.4 - - + -
51A LYS* 3.8 47.8 - - + +
54A ALA* 4.0 13.2 - - + -
55A TYR* 4.2 19.5 - - + +
59A ALA* 3.9 16.8 - - + -
61A TYR* 1.3 81.4 - - - +
63A GLU* 1.3 59.8 + - - +
64A GLN* 2.9 22.1 + - - +
151A GLU* 4.5 0.2 - - - +
154A PHE* 4.9 2.0 - - + -
155A VAL* 3.8 25.8 - - + -
166A ILE* 3.9 15.0 - - + -
167A GLY 2.9 9.6 + - - +
168A ILE* 3.4 1.4 - - - -
169A TYR* 2.9 17.3 + - - -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 4.3 8.9 - - + +
35A ALA 3.2 22.6 + - - +
36A HIS* 3.4 13.4 - - - -
37A ARG* 3.0 28.3 + - - +
46A HIS* 3.4 4.8 - - - -
51A LYS* 3.1 28.7 + - - +
61A TYR 4.1 0.4 - - - -
62A LEU* 1.3 72.1 - - - +
64A GLN* 1.3 65.1 + - - +
65A ASP* 3.9 6.3 - - - -
169A TYR* 3.3 18.4 - - - +
208A GLN* 2.9 17.3 + - - +
344A PHE* 3.9 10.8 - - + -
902A GOL 3.1 6.6 + - - -
904A CA 2.4 29.4 - - - -
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Residues in contact with GLN 64 (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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46A HIS* 3.7 4.3 - - - -
62A LEU* 2.9 23.4 + - - +
63A GLU* 1.3 77.7 - - - +
65A ASP* 1.3 63.4 - - - +
66A LEU* 4.0 16.6 - - + -
76A VAL* 4.1 5.4 - - + -
148A PHE* 4.0 19.6 - - + -
151A GLU* 2.8 40.9 + - + +
155A VAL* 5.1 0.2 - - - +
168A ILE* 3.6 19.8 - - - +
169A TYR 3.2 10.3 + - - +
170A PRO* 3.1 28.2 - - + +
171A GLU 2.8 27.6 + - - -
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Residues in contact with ASP 65 (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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37A ARG* 3.8 9.4 + - - +
46A HIS* 2.7 29.4 + - - +
63A GLU* 3.4 4.8 - - - +
64A GLN* 1.3 75.0 - - - +
66A LEU* 1.3 60.3 + - - +
76A VAL* 3.1 9.0 - - - +
77A LEU 3.0 39.8 + - - +
78A HIS* 3.5 20.9 - - - +
171A GLU* 3.1 14.1 - - - +
173A LYS* 3.8 8.3 - - + -
904A CA 2.5 29.6 - - - -
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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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64A GLN* 4.0 11.4 - - + -
65A ASP* 1.3 83.3 - - - +
67A VAL* 1.3 68.5 + - - +
74A LEU* 4.5 8.3 - - + -
75A VAL 3.5 8.7 - - - +
76A VAL* 4.2 5.4 - - + -
148A PHE* 3.7 62.4 - - + -
170A PRO* 4.0 8.1 - - + -
171A GLU 2.9 19.8 + - - +
172A ILE* 4.7 1.1 - - + -
173A LYS* 3.0 25.0 + - - +
185A ILE* 3.2 13.5 - - + +
189A THR* 3.8 23.8 - - + +
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Residues in contact with VAL 67 (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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65A ASP 4.4 0.2 + - - -
66A LEU* 1.3 79.7 - - - +
68A MET* 1.3 64.2 + - - +
74A LEU* 3.4 3.2 - - - -
75A VAL* 2.9 48.8 + - + -
77A LEU* 3.9 26.2 - - + +
79A ASP 3.7 26.9 - - - +
80A HIS* 4.0 10.5 - - + -
104A ALA* 3.9 13.0 - - + -
173A LYS* 3.8 13.7 - - + -
178A HIS* 3.7 9.0 - - + +
185A ILE* 3.5 7.2 - - - -
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Residues in contact with MET 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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67A VAL* 1.3 76.5 - - - +
69A THR* 1.3 65.3 + - - +
72A ASP* 3.8 41.7 - - + +
73A ASN 3.2 4.7 - - - +
74A LEU* 3.6 20.9 - - + -
104A ALA* 3.8 5.0 - - - +
105A ILE* 3.4 25.6 + - - +
178A HIS* 3.0 20.9 + - + -
183A LYS* 3.9 24.2 - - + -
184A ASP 4.2 3.1 - - - +
185A ILE* 3.6 34.1 - - + -
188A LYS* 4.2 16.8 - - + -
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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