Contacts of the strand formed by residues 37 - 45 (chain B) 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 VAL 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.5 8.8 - - - +
35B GLY 5.1 0.2 - - - +
36B GLU* 1.3 79.5 - - - +
38B LEU* 1.3 59.2 + - - +
39B LEU* 3.7 28.5 - - + -
71B VAL* 4.0 9.2 - - + -
73B GLU 3.3 8.3 - - - +
74B SER* 3.6 23.1 - - - +
76B ASN* 4.1 6.5 - - + -
79B LEU* 3.9 25.8 - - + +
95B SER 3.8 0.2 - - - +
96B ILE* 3.4 5.2 - - - -
97B SER* 2.8 43.8 + - - +
99B GLY 5.2 0.4 - - - +
102B LEU* 4.3 9.0 - - + -
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Residues in contact with LEU 38 (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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2B SER* 3.9 18.4 - - - +
29B LEU* 3.9 25.8 - - + -
32B LEU* 3.8 8.9 - - + +
37B VAL* 1.3 71.2 - - - +
39B LEU* 1.3 64.1 + - - +
71B VAL* 3.5 4.5 - - - -
72B VAL* 2.9 46.6 + - + +
73B GLU* 2.7 37.8 + - + +
94B HIS* 4.5 11.0 - - + -
95B SER 3.4 20.0 - - - +
96B ILE* 4.2 7.0 - - + -
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Residues in contact with LEU 39 (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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37B VAL* 3.7 17.0 - - + -
38B LEU* 1.3 73.5 - - - +
40B GLU* 1.3 60.2 + - - +
41B ALA 4.1 0.2 - - - -
67B GLN* 4.9 2.2 - - - +
69B ALA* 4.0 10.5 - - + -
70B LYS 3.5 1.6 - - - +
71B VAL* 3.6 35.0 - - + +
72B VAL* 4.7 2.0 - - - -
85B VAL* 4.0 17.9 - - + -
87B ALA* 3.7 16.8 - - + -
94B HIS* 3.1 10.2 - - - +
95B SER* 2.7 53.3 + - - +
97B SER* 4.1 9.0 - - - -
102B LEU* 3.7 29.2 - - + -
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Residues in contact with GLU 40 (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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38B LEU 4.2 0.2 + - - -
39B LEU* 1.3 73.6 - - - +
41B ALA* 1.3 73.8 + - - +
42B LEU* 3.4 4.4 + - + +
69B ALA* 3.3 3.2 - - - -
70B LYS* 2.9 37.6 + - + +
72B VAL* 3.9 24.3 - - + +
93B THR 3.5 4.9 - - - +
94B HIS* 2.9 34.8 + - + +
282C LYS* 3.1 27.5 + - - +
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Residues in contact with ALA 41 (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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40B GLU* 1.3 81.7 - - - +
42B LEU* 1.3 61.2 + - - +
44B LEU* 4.0 19.1 - - + -
67B GLN* 3.2 38.0 + - + +
68B VAL 3.8 3.1 - - - -
92B THR 3.7 7.0 - - - +
93B THR* 2.7 21.7 + - - +
329B ALA* 3.5 15.5 - - + +
282C LYS* 5.7 0.3 + - - -
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Residues in contact with LEU 42 (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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40B GLU* 4.1 9.0 - - - +
41B ALA* 1.3 77.2 - - - +
43B PHE* 1.3 84.2 + - + +
68B VAL* 2.9 14.8 + - + +
69B ALA 4.4 2.9 - - - -
70B LYS* 4.1 20.0 - - + +
84B ILE* 4.1 26.5 - - + -
115B LEU* 4.2 17.7 - - + -
328B LYS* 4.0 2.4 - - - +
329B ALA* 3.2 23.9 + - - +
282C LYS* 3.8 35.4 - - + +
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Residues in contact with PHE 43 (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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42B LEU* 1.3 95.5 - - + +
44B LEU* 1.3 62.5 + - - +
67B GLN* 3.2 5.0 - - - +
68B VAL* 2.8 36.3 + - + -
114B PRO* 5.8 2.7 - - + -
115B LEU* 4.3 26.0 - - + -
116B SER* 3.7 29.2 - - - -
119B LEU* 3.5 15.1 - - + +
302B ILE* 5.5 6.5 - - + -
326B ILE* 3.7 21.3 - - + -
327B VAL 3.4 4.3 - - - +
328B LYS* 3.9 35.9 - - + -
286C ASP* 6.0 0.4 - - - -
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Residues in contact with LEU 44 (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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41B ALA* 4.0 7.6 - - + -
43B PHE* 1.3 78.4 - - - +
45B THR* 1.3 61.4 + - - +
66B GLN 3.9 6.1 - - - +
67B GLN* 3.7 19.5 - - + +
90B GLY 4.4 2.9 - - - +
92B THR 3.6 27.6 - - - +
119B LEU* 3.9 4.1 - - - +
306B PHE* 4.0 18.2 - - + -
309B MET* 3.8 32.5 - - + -
326B ILE* 3.7 4.2 - - - +
327B VAL* 2.8 48.7 + - + +
329B ALA* 4.0 24.9 - - + -
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Residues in contact with THR 45 (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 LEU* 1.3 74.5 - - - +
46B VAL* 1.3 65.3 + - - +
47B ASP* 2.7 26.6 + - - +
49B TYR* 5.8 0.4 - - - +
50B MET* 3.5 11.2 - - + +
65B GLY* 5.1 0.2 - - - -
66B GLN* 3.1 42.7 + - + +
91B TRP* 5.0 0.2 - - - -
119B LEU* 3.9 19.7 - - + +
309B MET* 3.5 10.0 - - - +
324B LYS* 2.7 31.9 + - - -
325B THR 4.2 4.3 - - - -
326B ILE* 4.8 0.4 - - - -
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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