Contacts of the strand formed by residues 55 - 61 (chain A) in PDB entry 1YLA
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 ARG 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU* 3.6 28.6 + - - +
43A ILE 3.5 5.8 - - - +
44A ALA* 5.1 6.3 - - + -
53A GLY 4.7 0.4 - - - +
54A GLY* 1.3 77.4 - - - +
56A TYR* 1.3 62.5 + - - +
57A GLN* 4.1 1.3 + - - +
77A THR* 3.8 8.1 + - - +
153A ALA* 3.1 20.9 + - - +
53B GLY* 2.8 22.8 + - - -
55B ARG* 3.3 57.4 - - - +
153B ALA 2.7 29.1 + - - -
154B GLY* 3.4 17.3 + - - -
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Residues in contact with TYR 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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42A GLU* 3.0 6.8 - - - +
43A ILE* 2.7 48.8 + - + +
45A GLY* 4.1 3.8 - - - -
51A TYR* 3.5 30.7 + - + +
54A GLY 3.9 15.7 - - - -
55A ARG* 1.3 72.1 - - - +
57A GLN* 1.3 63.0 + - - +
58A LEU* 3.7 2.4 + - - +
75A PHE* 3.7 33.7 - + + -
77A THR* 3.7 19.1 - - + -
78A LYS 4.0 14.1 - - - -
79A ILE* 4.0 15.1 - - + +
117A LEU* 4.0 15.7 - - + -
149A ALA* 3.3 32.6 - - - +
153A ALA* 3.3 19.1 - - + +
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Residues in contact with GLN 57 (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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40A ARG* 3.9 24.0 - - - +
41A GLY 3.3 9.2 - - - +
42A GLU* 3.7 23.2 - - + +
55A ARG 4.1 1.5 + - - +
56A TYR* 1.3 73.8 - - - +
58A LEU* 1.3 56.9 + - - +
75A PHE* 3.7 3.8 - - - +
76A ILE* 2.7 48.8 + - + +
77A THR* 2.8 21.2 + - - +
57B GLN* 2.7 35.4 + - - +
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Residues in contact with LEU 58 (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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40A ARG* 3.3 16.5 - - - -
41A GLY 2.8 27.0 + - - +
42A GLU 4.4 3.6 - - - +
43A ILE* 4.0 14.8 - - + -
56A TYR 4.0 5.8 - - - +
57A GLN* 1.3 76.8 - - - +
59A GLU* 1.3 60.9 - - - +
60A ILE* 3.8 14.1 - - + -
73A VAL* 4.1 11.0 - - + -
74A ARG 3.4 7.0 - - - +
75A PHE* 3.7 45.1 - - + -
76A ILE* 3.6 3.4 - - - -
110A LEU* 3.3 33.0 - - + -
113A LEU* 3.7 17.3 - - + -
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Residues in contact with GLU 59 (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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38A GLU* 4.1 18.9 - - - +
39A LEU 4.2 2.0 - - - -
40A ARG* 5.0 2.9 - - - +
58A LEU* 1.3 72.9 - - - +
60A ILE* 1.3 60.3 + - - +
61A LYS* 4.2 31.1 + - + +
72A LYS 3.1 14.9 - - - +
73A VAL* 3.5 1.9 - - - -
74A ARG* 2.9 64.2 + - + +
76A ILE* 3.3 19.8 - - + +
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.8 4.5 - - + -
38A GLU* 3.1 6.9 - - - +
39A LEU* 2.8 54.6 + - + +
40A ARG 4.6 0.2 - - - -
41A GLY* 4.0 15.5 - - - +
58A LEU* 3.8 17.7 - - + -
59A GLU* 1.3 79.0 - - - +
61A LYS* 1.3 62.9 + - - +
62A ILE* 3.9 7.4 - - + -
71A PRO* 3.9 20.4 - - + -
72A LYS 3.8 1.3 - - - -
73A VAL* 3.7 26.9 - - + -
106A LEU* 3.9 27.1 - - + -
109A VAL* 5.9 1.8 - - + -
110A LEU* 5.0 6.5 - - + -
113A LEU* 5.7 0.2 - - + -
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Residues in contact with LYS 61 (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 THR 3.3 7.0 - - - +
38A GLU* 3.9 26.5 - - + -
59A GLU* 4.2 29.7 + - + +
60A ILE* 1.3 78.3 - - - +
62A ILE* 1.3 65.1 + - - +
63A PRO* 3.5 1.4 - - - +
71A PRO* 3.4 3.1 - - - +
72A LYS* 2.9 53.1 + - + +
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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