Contacts of the strand formed by residues 19 - 28 (chain B) in PDB entry 1YBY
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 ILE 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B THR* 4.5 4.3 - - - -
13B PHE 3.4 4.0 - - - +
14B GLU* 3.8 26.7 - - + +
17B GLY 5.7 1.3 - - - +
18B GLN* 1.3 80.4 - - - +
20B PHE* 1.3 68.1 + - - +
43B ASN* 3.8 8.1 + - - +
44B ILE* 3.1 39.8 + - + -
45B VAL* 4.4 11.1 + - + +
63B ALA* 3.5 26.7 - - + -
64B HIS 5.6 0.2 - - - +
65B ILE* 4.8 2.2 - - + -
116B HIS* 3.4 39.7 - - + +
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Residues in contact with PHE 20 (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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11B VAL 3.9 0.2 - - - +
12B THR* 3.2 7.1 - - - -
13B PHE* 3.0 53.9 + + + -
15B LEU* 3.5 50.3 - - + -
16B ASP* 5.3 4.9 - - + -
18B GLN* 4.6 4.5 - - - -
19B ILE* 1.3 75.0 - - - +
21B GLN* 1.3 59.2 + - - +
41B LEU* 3.9 22.2 - - + -
42B LYS 3.2 4.7 - - - -
43B ASN* 3.8 43.1 - - + -
44B ILE* 4.3 3.8 - - - -
48B ALA 5.6 0.2 - - - -
50B ILE* 4.1 22.4 - - + -
52B LYS* 5.7 2.9 - - - -
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Residues in contact with GLN 21 (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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10B GLY* 3.5 38.3 + - - +
11B VAL 3.4 3.4 - - - -
12B THR* 3.9 5.2 - - + -
20B PHE* 1.3 75.1 - - - +
22B VAL* 1.3 70.4 + - - +
23B ILE* 3.2 5.1 + - - +
41B LEU* 3.3 5.4 - - - -
42B LYS* 2.7 49.2 + - + +
44B ILE* 3.6 21.5 - - + +
114B LEU* 6.1 0.2 - - - +
121B PHE* 3.4 37.0 + - - +
122B GLY* 5.1 3.2 - - - -
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Residues in contact with VAL 22 (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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7B PHE* 4.1 15.5 - - + -
8B LYS 3.8 13.5 - - - +
9B ASN* 4.3 1.7 - - - +
10B GLY* 2.8 27.7 + - - -
11B VAL* 3.1 30.9 + - + +
13B PHE* 3.9 20.0 - - + -
21B GLN* 1.3 74.5 - - - +
23B ILE* 1.3 62.5 + - - +
24B GLU 4.0 12.1 - - - +
25B PHE* 3.6 33.4 - - + -
39B THR* 5.0 0.7 - - - -
40B LYS 3.9 3.4 - - - +
41B LEU* 4.0 9.2 - - + -
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Residues in contact with ILE 23 (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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9B ASN* 3.2 24.3 + - - +
21B GLN* 4.0 3.8 - - - +
22B VAL* 1.3 72.5 - - - +
24B GLU* 1.3 67.6 + - + +
40B LYS* 2.8 31.0 + - + +
41B LEU 3.8 4.0 - - - +
42B LYS* 3.7 43.1 - - + +
49B THR* 3.8 18.2 - - + +
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Residues in contact with GLU 24 (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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146A THR* 2.5 34.9 + - - +
147A GLY* 3.5 15.7 + - - -
9B ASN* 3.6 12.3 - - - +
22B VAL* 4.0 1.1 - - - +
23B ILE* 1.3 83.4 - - + +
25B PHE* 1.3 66.1 + - - +
39B THR* 3.4 1.2 - - - -
40B LYS* 2.7 61.3 + - + +
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Residues in contact with PHE 25 (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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146A THR* 3.4 15.4 + - - +
4B ALA 5.5 1.1 - - - -
7B PHE* 3.2 41.1 - - + -
8B LYS* 3.9 4.5 - - + -
9B ASN* 3.7 24.4 + - - -
22B VAL* 3.6 19.1 - - + -
24B GLU* 1.3 77.9 - - - +
26B GLN* 1.3 61.7 + - - +
27B HIS* 3.9 23.8 - - + -
37B VAL* 3.9 13.0 - - + -
38B ARG 3.0 13.7 - - - +
39B THR* 3.9 15.3 - - + -
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Residues in contact with GLN 26 (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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144A THR* 3.4 19.2 + - - +
145A ALA 3.0 17.3 + - - +
146A THR 3.8 5.8 - - - +
147A GLY 2.8 27.5 + - - +
148A ALA* 4.9 3.2 - - + +
164A LEU* 4.8 7.1 - - - +
25B PHE* 1.3 81.3 - - - +
27B HIS* 1.3 62.0 + - - +
28B VAL* 3.5 14.8 + - + +
36B PHE 3.8 0.2 - - - +
37B VAL* 3.4 1.2 - - - -
38B ARG* 2.8 62.3 + - + +
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Residues in contact with HIS 27 (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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4B ALA 5.1 0.2 + - - -
5B GLY* 4.0 22.6 + - - -
25B PHE* 3.9 19.0 - - + -
26B GLN* 1.3 71.2 - - - +
28B VAL* 1.3 70.3 + - - +
29B LYS* 3.9 22.9 + - + +
35B ALA* 4.4 2.0 - - - +
36B PHE 3.7 9.9 - - - -
37B VAL* 4.0 14.5 - - + +
56B PRO* 3.6 31.6 - - + +
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Residues in contact with VAL 28 (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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26B GLN* 4.0 17.3 - - + +
27B HIS* 1.3 74.6 - - - +
29B LYS* 1.3 64.4 + - - +
30B PRO* 3.3 13.9 - - + +
35B ALA* 3.3 7.6 - - - +
36B PHE* 2.9 72.2 + - + +
38B ARG* 4.0 17.5 - - - +
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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