Contacts of the strand formed by residues 50 - 56 (chain A) in PDB entry 1YH2
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLN* 3.3 40.2 - - + +
38A ILE 4.1 2.7 - - - -
39A LEU* 4.1 13.9 - - + -
48A LYS 4.4 6.5 - - - +
49A GLY* 1.3 76.7 - - - +
51A PHE* 1.3 61.8 + - - +
52A LYS* 4.1 0.8 + - + -
72A THR* 3.9 6.8 + - - +
151A ALA* 2.8 27.3 + - - +
153A GLN* 4.5 18.6 + - - +
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Residues in contact with PHE 51 (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 GLN* 3.2 5.8 - - - -
38A ILE* 2.8 50.8 + - + +
40A GLY* 4.0 2.0 - - - -
46A TYR* 3.7 44.0 - + + -
49A GLY 3.9 10.8 - - - -
50A VAL* 1.3 75.2 - - - +
52A LYS* 1.3 61.5 + - - +
53A LEU* 3.5 2.9 - - - +
70A PHE* 3.8 19.5 - + + -
72A THR* 3.7 16.2 - - + -
73A PRO 3.8 15.5 - - - -
74A ILE* 3.8 23.3 - - + -
115A MET* 3.7 15.9 - - + -
147A THR* 4.0 12.8 - - + -
151A ALA* 3.6 22.0 - - + -
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Residues in contact with LYS 52 (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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25A TRP* 4.2 24.5 - - + -
27A ASP* 5.6 1.8 + - - -
35A ARG* 4.4 16.1 - - - +
36A ALA 3.4 11.2 - - - +
37A GLN* 4.5 2.9 - - + +
50A VAL* 4.1 1.6 + - + +
51A PHE* 1.3 74.5 - - - +
53A LEU* 1.3 62.6 + - - +
70A PHE* 3.7 2.8 - - - -
71A LEU* 2.8 53.4 + - + +
72A THR* 2.8 20.8 + - - +
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Residues in contact with LEU 53 (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 ARG* 3.4 9.2 - - - +
36A ALA* 3.0 46.3 + - + +
38A ILE* 3.8 27.6 - - + +
51A PHE 3.5 19.3 - - - +
52A LYS* 1.3 77.1 - - - +
54A GLU* 1.3 58.6 - - - +
68A ILE* 3.6 28.9 - - + -
69A ARG 3.2 9.4 - - - +
70A PHE* 3.8 38.8 - - + -
71A LEU* 3.9 7.7 - - - +
85A ILE* 4.1 1.8 - - + -
108A LEU* 5.0 1.1 - - + -
111A ILE* 4.2 10.3 - - + -
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Residues in contact with GLU 54 (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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33A ASP* 5.0 0.2 - - - +
34A LEU 3.9 3.4 - - - -
35A ARG* 3.9 24.0 + - - +
53A LEU* 1.3 73.0 - - - +
55A VAL* 1.3 62.7 + - - +
56A ILE* 3.8 33.7 - - + +
67A GLN 3.6 1.4 - - - +
68A ILE* 3.3 8.0 - - - +
69A ARG* 2.8 71.9 + - + +
71A LEU* 3.8 19.6 - - + +
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Residues in contact with VAL 55 (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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24A CYS* 4.7 2.9 - - - -
32A ASP 3.9 0.2 - - - +
34A LEU* 2.8 60.6 + - + +
35A ARG 4.5 0.7 - - - -
36A ALA* 3.9 30.1 - - + +
53A LEU 4.6 0.7 - - - +
54A GLU* 1.3 78.9 - - - +
56A ILE* 1.4 59.6 + - - +
57A ILE* 3.8 23.1 - - + -
66A PRO* 4.3 4.7 - - + -
67A GLN 3.7 2.5 - - - -
68A ILE* 4.0 29.6 - - + -
104A ILE* 4.4 9.6 - - + -
108A LEU* 4.2 5.8 - - + -
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Residues in contact with ILE 56 (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 ASP 3.6 5.8 - - - +
33A ASP* 3.4 31.2 - - - +
54A GLU* 3.8 35.2 - - + +
55A VAL* 1.4 74.0 - - - +
57A ILE* 1.3 67.8 + - - +
58A PRO* 3.5 3.4 - - + +
66A PRO* 3.7 1.9 - - - +
67A GLN* 2.8 65.9 + - + +
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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