Contacts of the strand formed by residues 128 - 133 (chain A) in PDB entry 3DAE
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 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS 3.3 1.0 - - - +
86A ILE* 2.8 55.2 + - + +
87A ASN* 5.9 0.9 - - - +
90A VAL* 5.9 5.2 - - + -
100A ILE* 4.8 12.6 - - + -
101A GLU* 4.4 17.0 - - - +
104A ILE* 4.3 12.1 - - + -
121A VAL* 4.0 23.8 - - + -
122A ILE 3.9 2.2 - - - -
123A LYS* 4.2 17.9 - - + +
124A SER 5.5 2.2 - - - +
126A ASP 4.8 3.6 - - - +
127A GLU* 1.3 77.0 - - - +
129A ILE* 1.3 61.5 + - - +
130A MET* 4.6 8.5 - - + -
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Residues in contact with ILE 129 (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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52A ILE* 5.8 8.3 - - + -
83A LEU* 4.2 26.5 - - + -
84A LYS 3.5 4.3 - - - +
85A ILE* 4.2 18.4 - - + -
120A ASP 4.1 0.2 - - - +
121A VAL* 3.5 3.6 - - - +
122A ILE* 2.8 62.1 + - + +
127A GLU* 3.6 31.4 - - + +
128A ILE* 1.3 77.6 - - - +
130A MET* 1.3 70.1 + - - +
131A VAL* 4.0 3.2 + - + +
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Residues in contact with MET 130 (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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82A ALA 3.2 1.2 - - - +
83A LEU* 3.0 11.3 - - - +
84A LYS* 2.9 47.8 + - + +
86A ILE* 4.2 21.5 - - + -
100A ILE* 4.6 6.5 - - - -
103A GLU* 4.4 9.2 - - + +
104A ILE* 3.7 37.0 - - + +
107A LEU* 4.2 24.9 - - + -
118A LEU* 4.2 10.8 - - + -
120A ASP 3.8 2.9 - - - -
121A VAL* 4.3 9.4 - - + +
128A ILE* 4.6 2.9 - - + -
129A ILE* 1.3 76.1 - - - +
131A VAL* 1.3 62.3 + - - +
132A ILE* 3.6 17.2 + - + -
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Residues in contact with VAL 131 (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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55A TYR* 3.4 37.7 - - + +
81A VAL* 3.6 17.3 - - + -
82A ALA 3.7 2.5 - - - -
83A LEU* 3.9 15.0 - - + -
118A LEU* 3.6 3.1 - - - +
119A TYR* 2.7 41.2 + - + -
120A ASP* 2.8 38.9 + - + +
122A ILE* 4.4 17.0 - - + -
129A ILE* 4.7 3.1 - - + +
130A MET* 1.3 72.5 - - - +
132A ILE* 1.3 58.0 + - - +
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 3.2 12.6 - - - +
82A ALA* 2.9 39.4 + - + +
84A LYS* 4.4 19.7 - - + -
107A LEU* 5.0 7.9 - - + -
116A ILE* 4.0 22.4 - - + -
117A LYS 3.4 11.9 - - - +
118A LEU* 4.6 6.7 - - + +
119A TYR* 4.1 2.0 - - - -
130A MET* 4.1 31.6 - - + -
131A VAL* 1.3 76.1 - - - +
133A GLU* 1.3 80.9 + - - +
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Residues in contact with GLU 133 (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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79A GLN* 3.8 14.2 + - - +
82A ALA* 4.7 2.3 + - - +
115A ILE 4.1 0.7 - - - +
116A ILE* 3.6 26.1 - - + +
117A LYS* 2.7 49.5 + - + +
119A TYR* 3.6 27.1 + - + +
132A ILE* 1.3 79.3 - - - +
134A TYR* 1.3 71.9 + - - +
135A ALA 3.8 1.0 + - - -
184A LEU* 5.7 0.5 - - - +
186A ASP* 5.6 2.6 - - - +
192A LYS* 3.6 32.6 + - - +
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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