Contacts of the strand formed by residues 43 - 48 (chain B) in PDB entry 1Y14
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 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B CYS* 3.4 6.7 - - - -
39B THR* 2.9 38.0 + - - -
40B GLY 4.2 0.6 + - - -
41B LYS 3.7 1.0 - - - -
42B PHE* 1.3 80.0 - - - +
44B TYR* 1.3 62.6 + - - -
45B ILE* 3.7 5.0 + - - +
79B PHE 3.4 8.7 - - - -
80B LYS* 4.2 11.0 - - - -
157B ILE* 4.6 8.5 - - - -
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Residues in contact with TYR 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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140A ASP* 3.2 37.5 - - - -
37B SER 3.7 4.0 - - - +
38B CYS* 3.9 21.5 - - + +
43B GLY* 1.3 71.7 - - - -
45B ILE* 1.3 60.2 + - - +
46B LEU* 3.2 20.5 + - + +
78B VAL* 3.0 8.4 - - - -
79B PHE* 2.8 44.8 + + - +
105B PRO* 3.6 37.3 + - + -
106B MET* 3.8 19.1 - - + +
157B ILE* 3.2 42.3 + - + +
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Residues in contact with ILE 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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7B LEU* 4.1 22.9 - - + -
34B VAL* 3.4 26.5 - - + +
35B GLU* 3.7 2.3 - - - -
36B GLY* 2.8 27.0 + - - -
37B SER* 3.0 24.5 + - - +
38B CYS* 5.6 0.2 - - - -
39B THR* 5.5 7.2 - - + -
42B PHE* 5.3 13.2 - - + -
43B GLY 4.5 6.5 - - - +
44B TYR* 1.3 70.1 - - - +
46B LEU* 1.3 59.8 + - - +
47B CYS 5.0 1.3 - - - +
48B VAL* 5.0 2.0 - - + -
74B TYR* 4.1 13.9 - - + +
76B ALA* 4.1 25.4 - - + -
77B VAL 4.2 2.5 - - - -
78B VAL* 4.4 6.7 - - + -
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Residues in contact with LEU 46 (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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59A ILE* 5.5 0.9 - - + -
138A ASN* 3.6 3.9 - - - +
140A ASP* 3.6 33.2 - - + -
141A LEU* 3.4 28.4 - - + +
144A THR* 3.5 31.2 - - + +
2B PHE* 4.0 15.9 - - + -
35B GLU* 3.6 10.9 - - - +
36B GLY* 4.7 2.2 - - - +
44B TYR* 3.2 14.6 + - + +
45B ILE* 1.3 72.8 - - - +
47B CYS* 1.3 64.2 + - + +
77B VAL* 3.1 17.3 + - + +
79B PHE* 3.7 30.3 - - + +
105B PRO* 3.7 7.6 - - + -
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Residues in contact with CYS 47 (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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59A ILE* 4.3 26.5 - - + -
62A ALA* 4.2 15.0 - - - -
63A LEU* 3.9 27.6 - - - -
66A ARG* 4.3 2.2 - - - -
141A LEU* 4.3 9.6 - - + -
35B GLU* 3.6 5.8 - - - +
45B ILE* 3.7 2.2 - - - +
46B LEU* 1.3 82.4 - - + +
48B VAL* 1.3 76.9 + - - +
49B LEU* 3.5 6.0 + - - +
76B ALA* 3.3 3.1 - - - -
77B VAL* 3.0 32.4 + - + -
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Residues in contact with VAL 48 (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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62A ALA* 4.3 3.3 - - - +
66A ARG* 3.0 19.0 + - - +
30B LEU* 4.3 2.5 - - + -
31B LEU* 3.5 34.5 - - + -
34B VAL* 4.0 15.0 - - + -
35B GLU* 3.1 14.3 + - + +
45B ILE* 5.0 2.0 - - + -
47B CYS* 1.3 80.2 - - - +
49B LEU* 1.3 69.9 + - - +
51B TYR* 5.3 2.7 + - + +
54B ILE* 4.1 17.7 - - + -
74B TYR* 3.9 30.5 - - + -
75B ARG 3.7 12.1 - - - +
76B ALA* 4.0 2.7 - - + -
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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