Contacts of the strand formed by residues 43 - 49 (chain N) in PDB entry 1YIT
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 43 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37N ARG 3.4 5.2 - - - +
38N LYS* 4.1 18.4 - - + +
42N HIS* 1.3 84.1 - - - +
44N ARG* 1.3 59.3 + - - +
62N HIS* 5.0 0.2 - - - -
63N SER* 2.9 36.4 + - - -
75N THR 4.6 4.7 - - - +
76N GLY* 4.6 4.9 - - - -
81N ALA* 4.1 18.6 - - + +
84N THR* 3.1 14.5 - - - +
114N LYS* 4.4 22.4 - - + +
118N ILE* 3.2 39.0 - - + -
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Residues in contact with ARG 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49 G 2.6 63.7 + - - +
59 G 3.4 20.0 + - - +
1209 A 4.0 15.6 + - - -
35N VAL 3.8 1.0 - - - +
36N ALA* 3.8 1.6 - - - -
37N ARG* 2.8 43.1 + - + +
38N LYS* 4.8 0.6 - - - +
42N HIS 4.4 0.2 - - - -
43N VAL* 1.3 73.8 - - - +
45N ALA* 1.3 64.9 + - - +
46N GLN* 3.9 34.1 - - + +
60N SER* 5.4 4.0 - - - -
61N ALA 3.4 11.0 - - - +
62N HIS* 3.4 39.9 + - + +
84N THR* 4.6 0.2 - - - -
118N ILE* 3.9 3.3 - - - +
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Residues in contact with ALA 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N LEU* 4.8 6.3 - - + -
35N VAL 3.4 6.1 - - - +
44N ARG* 1.3 75.6 - - - +
46N GLN* 1.3 61.2 - - - +
60N SER* 3.2 4.3 - - - -
61N ALA 2.8 35.3 + - - +
84N THR* 4.3 11.0 - - + +
85N GLY* 4.3 2.0 - - - -
88N ALA* 3.4 21.0 - - + +
118N ILE* 3.7 27.1 - - + -
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Residues in contact with GLN 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49 G 4.5 0.4 - - - +
59 G 2.4 67.1 + - - +
69 C 3.5 8.7 - - - +
1199 C 4.2 5.9 + - - -
34N LEU* 3.3 7.0 - - - +
35N VAL* 2.6 48.6 + - + +
44N ARG* 3.9 19.4 - - + +
45N ALA* 1.3 78.1 - - - +
47N LEU* 1.3 60.6 + - - +
48N VAL* 3.9 13.0 - - + -
57N THR* 4.1 9.2 + - + +
59N ALA 3.5 6.7 - - - +
60N SER* 4.0 12.6 - - - -
88N ALA* 5.8 0.4 - - - -
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Residues in contact with LEU 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N PRO* 5.1 6.1 - - + -
33N ARG 3.3 13.2 - - - +
34N LEU* 3.4 34.1 - - + -
46N GLN* 1.3 71.4 - - - +
48N VAL* 1.3 60.1 + - - +
56N ASP 3.7 0.3 - - - +
57N THR* 3.6 2.3 - - - -
58N LEU* 3.0 30.9 + - + +
59N ALA* 2.8 22.2 + - + +
88N ALA* 5.4 3.6 - - + +
92N ALA* 3.3 25.1 - - + -
97N VAL* 3.2 38.1 - - + -
100N ALA* 3.8 14.4 - - + -
127N LEU* 3.6 8.7 - - + -
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Residues in contact with VAL 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69 C 3.8 9.2 - - - +
32N PRO* 3.3 6.3 - - - +
33N ARG* 2.7 48.9 + - - +
35N VAL* 3.5 26.5 - - + -
46N GLN* 4.0 11.2 - - + +
47N LEU* 1.3 77.4 - - - +
49N THR* 1.3 66.9 + - - +
55N ASP* 3.1 39.9 - - + -
56N ASP 3.1 11.2 - - - +
57N THR* 3.9 15.3 - - - +
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Residues in contact with THR 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N PRO* 4.1 18.5 - - + +
48N VAL* 1.3 78.8 + - - +
50N LEU* 1.3 85.8 + - + +
55N ASP* 3.3 6.6 - - - +
56N ASP* 2.7 34.6 + - + -
58N LEU* 3.4 31.8 - - + +
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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