Contacts of the strand formed by residues 67 - 74 (chain A) in PDB entry 2Y05
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 GLN 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 4.9 2.6 - - - +
41A ALA* 3.4 27.8 + - + +
43A PHE 3.1 15.5 - - - +
44A LEU* 3.6 16.9 - - + +
66A GLN* 1.3 77.8 - - - +
68A VAL* 1.3 65.8 + - - +
69A ALA* 3.6 13.8 - - + +
86A LEU* 3.5 6.8 - - - +
87A ALA* 2.8 40.0 + - + +
89A PRO* 3.6 27.6 - - + +
90A GLY 3.7 5.5 + - - -
92A THR* 3.0 26.2 + - - +
93A THR 4.9 0.7 - - - +
95A SER* 4.7 4.3 + - - -
119A LEU* 4.1 6.3 - - - -
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Residues in contact with VAL 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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41A ALA* 3.8 1.7 - - - -
42A LEU* 2.8 35.7 + - + +
43A PHE* 2.8 21.8 + - + +
67A GLN* 1.3 71.8 - - - +
69A ALA* 1.3 62.4 + - - +
84A ILE* 3.6 28.3 - - + -
85A VAL 3.5 4.9 - - - +
86A LEU* 4.0 9.4 - - + -
105A LEU* 5.7 2.0 - - + -
115A LEU* 3.7 35.9 - - + +
118A ALA* 3.9 16.4 - - + -
119A LEU* 4.0 14.8 - - + +
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Residues in contact with ALA 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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39A LEU* 3.8 28.5 - - + -
40A GLU 3.3 13.0 - - - +
42A LEU* 4.3 5.4 - - - +
67A GLN* 3.6 21.8 - - + +
68A VAL* 1.3 73.6 - - - +
70A LYS* 1.3 59.6 - - - +
84A ILE* 3.3 6.1 - - - +
85A VAL* 2.7 44.0 + - + +
87A ALA* 4.8 1.1 - - + -
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Residues in contact with LYS 70 (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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39A LEU* 3.5 4.9 - - - -
40A GLU* 2.8 37.8 + - + +
42A LEU* 4.1 18.1 - - + +
69A ALA* 1.3 74.5 - - - +
71A VAL* 1.3 68.0 + - - +
72A VAL* 3.4 12.6 + - + -
82A GLY* 3.8 27.4 - - - +
83A THR 3.3 3.4 - - - -
84A ILE* 3.8 21.3 - - + -
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Residues in contact with VAL 71 (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 VAL* 3.7 19.5 - - + -
38A LEU 3.6 4.3 - - - +
39A LEU* 3.6 17.7 - - + -
70A LYS* 1.3 73.4 - - - +
72A VAL* 1.3 58.0 + - - +
73A GLU 3.5 23.8 - - - +
74A SER* 4.0 4.9 - - - -
79A LEU* 4.0 17.7 - - + +
80A PRO 3.6 20.0 - - - +
81A LYS* 3.5 4.2 - - - +
82A GLY* 2.7 27.9 + - - -
83A THR* 2.8 31.3 + - - +
85A VAL* 4.7 8.3 - - + -
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Residues in contact with VAL 72 (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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38A LEU* 2.8 44.3 + - + +
39A LEU 4.8 0.2 - - - -
40A GLU* 3.5 43.3 - - + +
70A LYS* 3.4 14.1 + - + +
71A VAL* 1.3 76.7 - - - +
73A GLU* 1.3 65.7 + - + +
81A LYS* 3.5 19.8 - - - +
94A HIS* 5.1 4.3 - - + -
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Residues in contact with GLU 73 (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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32A LEU* 3.6 16.6 - - + -
37A VAL* 3.3 4.5 - - - +
38A LEU* 2.8 46.7 + - + -
71A VAL* 3.5 2.8 - - - +
72A VAL* 1.3 87.1 - - + +
74A SER* 1.3 63.0 + - - +
81A LYS* 4.3 6.3 - - + -
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Residues in contact with SER 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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32A LEU* 3.7 3.1 - - - +
36A GLU 3.9 4.3 - - - -
37A VAL* 3.6 6.8 - - - +
71A VAL* 4.0 4.7 - - - -
73A GLU* 1.3 76.7 - - - +
75A LYS* 1.3 64.1 + - - +
76A ASN 2.9 20.1 + - - -
79A LEU 2.7 29.0 + - - -
80A PRO* 4.5 1.1 - - - +
81A LYS* 4.5 13.2 - - - +
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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