Contacts of the strand formed by residues 123 - 130 (chain B) in PDB entry 2DXU
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 LYS 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B ALA 2.8 20.1 + - - +
27B LYS* 3.5 13.5 + - - +
29B SER 2.7 29.9 + - - -
30B TYR* 4.6 3.8 - - - +
31B LEU* 4.6 7.0 - - - +
65B VAL* 3.5 34.1 - - + -
66B LEU 3.6 4.0 - - - +
67B SER* 5.1 2.0 - - - +
118B GLU 4.1 0.2 - - - +
119B GLY* 3.6 1.7 - - - -
120B LYS* 2.8 67.0 + - - +
121B GLY 4.3 0.9 - - - +
122B ASP* 1.3 81.0 - - - +
124B ILE* 1.3 67.5 - - - +
125B VAL* 4.7 4.4 - - + +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ILE 3.5 1.7 - - - +
65B VAL* 3.7 2.4 - - - -
66B LEU* 2.8 47.3 + - + +
68B PRO* 3.5 22.2 - - + -
75B LEU* 3.4 41.3 - - + -
78B ILE* 4.2 20.4 - - + -
117B VAL* 3.6 28.0 - - + -
118B GLU 3.7 4.7 - - - +
119B GLY* 4.9 5.8 - - - -
121B GLY 6.0 0.2 - - - +
122B ASP 5.1 2.7 - - - +
123B LYS* 1.3 78.1 - - - +
125B VAL* 1.3 65.8 + - - +
126B LEU 4.8 0.2 - - - +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASN* 3.5 31.9 - - - +
26B ALA* 3.8 34.1 - - + +
27B LYS* 3.7 28.3 - - + +
63B SER* 3.9 6.7 - - - -
64B ILE 3.5 4.7 - - - +
65B VAL* 5.1 1.8 - - + -
116B LEU 3.6 1.6 - - - +
117B VAL* 3.2 6.8 - - - +
118B GLU* 2.8 43.8 + - + +
120B LYS* 5.6 1.1 - - + -
123B LYS* 4.7 12.1 - - + +
124B ILE* 1.3 77.8 - - - +
126B LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 5.8 2.7 - - + -
23B ASN* 4.3 0.2 - - - -
62B LEU 4.0 0.3 - - - +
63B SER* 3.2 3.4 - - - -
64B ILE* 2.8 56.5 + - + +
66B LEU* 4.1 24.9 - - + -
78B ILE* 3.9 18.2 - - + +
81B LEU* 4.8 4.9 - - + -
82B GLY* 4.2 20.2 - - - +
115B VAL* 3.5 30.5 - - + -
116B LEU 4.1 0.7 - - - -
117B VAL* 3.7 15.3 - - + -
124B ILE 4.0 0.8 + - - -
125B VAL* 1.3 70.5 - - - +
127B GLY* 1.3 58.9 + - - +
128B ILE* 4.1 13.3 + - + +
164B LEU* 4.6 7.2 - - + -
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASN* 3.1 23.8 + - - -
62B LEU 3.4 5.8 - - - -
115B VAL* 3.3 6.8 - - - +
116B LEU 2.8 43.3 + - - -
126B LEU* 1.3 71.8 - - - +
128B ILE* 1.3 65.2 + - - +
2302B BT5 4.2 8.3 - - - -
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 3.5 4.7 - - + +
62B LEU* 2.8 50.6 + - + +
64B ILE* 4.8 0.4 - - + -
82B GLY* 3.9 22.9 - - - +
86B VAL* 3.7 25.1 - - + -
113B ALA* 5.3 0.2 - - + -
114B GLY 3.6 7.6 - - - +
115B VAL* 4.4 7.9 - - + -
126B LEU* 4.1 17.2 + - + +
127B GLY* 1.3 80.4 - - - +
129B GLY* 1.3 67.6 + - - +
130B LEU* 4.7 2.7 - - + +
160B LEU* 4.4 13.5 - - + -
164B LEU* 3.7 29.6 - - + -
2302B BT5 3.5 6.8 - - - +
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TRP* 3.6 14.0 - - - -
60B LEU 3.4 4.7 - - - -
61B TRP* 3.7 13.9 - - - -
113B ALA* 3.0 7.2 - - - +
114B GLY 2.9 34.8 + - - -
128B ILE* 1.3 74.1 - - - +
130B LEU* 1.3 59.7 + - - -
2302B BT5 3.6 12.4 - - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLY* 3.7 1.0 - - - -
60B LEU* 2.9 52.3 + - + +
61B TRP* 3.7 4.7 - - - -
86B VAL* 4.2 17.3 - - + -
89B THR* 5.1 6.1 - - + -
90B LEU* 4.3 11.7 - - + -
112B ILE* 3.5 26.5 - - + +
113B ALA* 3.8 12.8 - - + -
128B ILE* 4.1 8.3 - - + -
129B GLY* 1.3 73.7 - - - +
131B ASN* 1.3 72.8 + - - +
132B VAL* 3.3 4.7 + - + +
143B MET* 4.2 7.2 - - + -
156B VAL* 3.7 29.8 - - + -
160B LEU* 5.0 6.7 - - + -
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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