Contacts of the strand formed by residues 117 - 124 (chain A) in PDB entry 2DYY
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 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.0 0.2 - - - -
34A PRO* 3.3 22.2 - - + +
47A ILE* 4.2 8.5 - - + -
50A GLN* 4.0 26.6 + - + +
51A THR* 3.8 24.9 - - + +
54A VAL* 4.0 4.2 - - + +
77A VAL* 3.7 9.4 - - + -
78A TYR 3.3 10.8 - - - +
79A LEU* 5.0 3.8 - - + -
88A MET* 3.6 31.6 - - + -
111A LEU* 3.7 3.4 - - - -
115A VAL* 3.6 4.1 - - - +
116A LEU* 1.3 83.8 - - - +
118A GLU* 1.3 66.8 + - - +
119A ILE* 3.7 30.7 - - + -
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Residues in contact with GLU 118 (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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31A GLY* 4.2 11.3 - - - +
32A GLN 3.1 22.9 - - - +
33A ILE* 4.0 13.1 - - + +
54A VAL* 5.0 0.2 - - - -
78A TYR* 3.0 42.2 + - + +
111A LEU* 3.8 14.3 - - + +
112A PRO* 3.6 23.4 - - - +
117A ILE* 1.3 77.9 - - - +
119A ILE* 1.3 65.4 + - - +
103C ARG 5.4 0.3 - - - +
104C VAL* 4.1 10.5 - - - +
105C ALA 3.4 10.8 + - - +
106C VAL* 3.1 31.5 - - - +
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Residues in contact with ILE 119 (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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30A ALA 4.0 1.4 - - - +
31A GLY* 3.3 2.4 - - - -
32A GLN* 2.8 38.0 + - - +
51A THR* 4.9 1.6 - - + -
54A VAL* 3.7 14.6 - - + -
55A LEU* 3.4 28.7 - - + -
58A ILE* 3.8 16.8 - - + +
75A VAL* 3.3 30.5 - - + -
76A THR 3.4 4.9 - - - +
77A VAL* 4.1 15.0 - - + -
78A TYR* 5.6 0.2 - - - -
92A TYR* 4.6 10.5 - - + -
96A PHE* 6.1 0.4 - - + -
117A ILE* 3.7 26.7 - - + -
118A GLU* 1.3 81.7 - - - +
120A GLU* 1.3 63.5 + - - +
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Residues in contact with GLU 120 (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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29A ILE 4.0 8.5 - - - +
30A ALA 4.4 0.9 - - - -
31A GLY* 4.0 5.6 - - - -
58A ILE* 5.1 0.9 - - - -
74A LYS* 6.2 1.6 - - - -
75A VAL* 3.3 5.9 - - - +
76A THR* 3.0 55.8 + - + +
78A TYR* 3.1 26.3 + - + -
119A ILE* 1.3 75.4 - - - +
121A ALA* 1.3 64.2 + - - +
122A ILE* 6.0 1.0 - - - +
120B GLU* 5.6 0.7 - - - +
74C LYS* 2.9 35.3 + - - -
76C THR* 4.9 3.0 + - - +
104C VAL* 3.3 22.9 - - + +
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Residues in contact with ALA 121 (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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29A ILE* 3.0 53.5 + - + +
58A ILE* 4.7 14.8 - - + -
72A VAL* 4.1 10.3 - - + -
74A LYS 3.1 11.2 - - - +
75A VAL* 4.1 12.8 - - + -
96A PHE* 5.7 0.4 - - + -
120A GLU* 1.3 78.6 - - - +
122A ILE* 1.3 68.8 + - - +
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Residues in contact with ILE 122 (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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26A PHE* 4.0 25.8 - - + -
27A LEU 3.3 9.0 - - - +
28A PHE* 3.9 32.5 - - + -
29A ILE* 5.7 0.2 - - - -
72A VAL* 3.6 3.2 - - - -
73A ILE* 2.8 38.3 + - + +
74A LYS* 2.8 36.3 + - + +
120A GLU* 6.0 0.9 - - - +
121A ALA* 1.3 80.5 - - - +
123A ALA* 1.3 62.6 + - - +
28B PHE* 3.8 22.0 - - + -
122B ILE* 5.8 1.3 - - + -
74C LYS* 5.3 9.0 - - - +
122C ILE* 5.8 2.0 - - + -
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Residues in contact with ALA 123 (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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26A PHE* 3.4 8.7 - - - -
27A LEU* 2.9 35.4 + - + -
29A ILE* 5.2 1.8 - - + +
62A LEU* 3.7 21.1 - - + -
67A TYR* 3.4 26.7 - - + -
71A ASP 3.3 14.1 - - - +
72A VAL* 3.9 3.4 - - + +
73A ILE* 4.5 1.1 - - - -
121A ALA 4.3 0.2 - - - -
122A ILE* 1.3 76.2 - - - +
124A TYR* 1.3 63.5 + - - +
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Residues in contact with TYR 124 (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 ASN* 3.6 25.7 + - + -
26A PHE* 3.4 39.0 - + + -
67A TYR* 4.0 1.8 - - - -
71A ASP* 2.8 32.1 + - - +
73A ILE* 3.9 23.8 - - + +
123A ALA* 1.3 75.5 - - - +
125A LYS* 1.3 59.7 + - - +
126A GLU* 4.1 24.9 - - + +
1B MET 3.2 42.9 + - - -
2B LYS* 4.3 16.0 - - + +
23B ALA* 3.7 9.0 - - + -
24B GLY* 3.5 21.6 + - - -
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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