Contacts of the strand formed by residues 110 - 119 (chain A) 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 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.1 5.1 - - - -
107A VAL 2.9 34.7 + - - +
108A ASN* 3.9 17.1 - - - +
109A TYR* 1.3 80.8 - - - +
111A LYS* 1.3 62.8 + - - +
112A ILE 3.3 0.9 + - - -
139A GLY* 3.7 13.2 - - - +
140A ALA 4.2 11.4 - - - +
141A THR* 3.7 17.2 + - + +
146A GLU* 3.4 25.2 + - - -
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Residues in contact with LYS 111 (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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53A TRP* 3.7 15.3 - - - -
100A LYS* 6.5 0.2 - - + -
104A ASP* 2.8 35.4 + - + +
105A VAL 4.2 1.8 - - - +
106A LEU* 3.6 17.3 - - + +
109A TYR 4.1 0.6 + - - -
110A LYS* 1.3 68.6 - - - +
112A ILE* 1.3 59.6 + - - +
113A ALA 3.7 18.2 - - - +
139A GLY 3.0 17.8 + - - +
140A ALA* 3.2 9.7 - - - +
141A THR 3.0 20.8 + - - +
2301B BT5 2.9 68.9 + - + +
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Residues in contact with ILE 112 (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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90A LEU* 3.9 19.5 - - + -
95A ILE* 4.5 3.4 - - + -
105A VAL* 2.9 35.4 + - + +
107A VAL* 3.9 23.1 - - + -
110A LYS 3.3 1.4 + - - -
111A LYS* 1.3 75.0 - - - +
113A ALA* 1.3 64.2 + - + +
130A LEU* 3.5 3.9 - - + +
131A ASN* 3.0 44.0 + - - +
141A THR* 3.6 25.8 - - + +
142A SER* 3.6 23.1 - - - +
143A MET* 3.6 17.3 - - + +
146A GLU* 4.7 0.7 - - + -
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Residues in contact with ALA 113 (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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53A TRP* 4.2 7.4 - - - -
86A VAL* 3.9 22.9 - - + -
104A ASP* 3.7 3.3 - - - -
105A VAL* 3.1 32.7 + - + +
111A LYS* 3.6 9.0 - - - +
112A ILE* 1.3 82.9 - - + +
114A GLY* 1.3 60.4 + - - +
115A VAL* 6.0 0.4 - - + -
128A ILE* 5.2 0.2 - - + -
129A GLY 3.1 15.5 - - - +
130A LEU* 3.8 18.2 - - + -
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Residues in contact with GLY 114 (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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53A TRP* 3.7 8.1 - - - -
103A ASN 3.6 6.1 - - - -
104A ASP* 4.1 1.8 - - - -
111A LYS* 4.2 0.2 - - - -
113A ALA* 1.3 74.9 - - - +
115A VAL* 1.3 65.1 + - - +
128A ILE* 3.6 3.6 - - - +
129A GLY 3.0 31.7 + - - +
2301B BT5 3.4 28.2 - - - +
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Residues in contact with VAL 115 (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 VAL* 3.7 27.7 - - + +
82A GLY* 3.9 7.9 - - - +
83A ALA* 3.7 26.9 - - - +
86A VAL* 5.1 3.1 - - + -
103A ASN* 2.9 44.9 + - + +
105A VAL* 5.4 3.1 - - + -
113A ALA* 6.0 0.2 - - + -
114A GLY* 1.3 78.6 - - - +
116A LEU* 1.3 64.9 + - - +
117A VAL* 4.3 0.7 - - + -
126A LEU* 3.5 25.6 - - + -
127A GLY 3.3 10.8 - - - +
128A ILE* 4.5 9.6 - - + -
2301B BT5 3.8 2.8 - - - +
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Residues in contact with LEU 116 (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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23A ASN* 3.4 16.4 + - - +
46A HIS* 3.5 43.1 - - + +
47A GLY 3.5 11.0 - - - +
48A ALA* 4.0 28.3 - - + +
79A VAL* 5.6 0.2 - - - -
103A ASN* 5.8 1.3 - - - +
115A VAL* 1.3 76.1 - - - +
117A VAL* 1.3 68.6 + - - +
118A GLU* 3.7 14.6 - - + +
127A GLY* 2.8 35.9 + - - +
2301B BT5 3.8 18.1 - - + +
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Residues in contact with VAL 117 (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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75A LEU 5.6 2.0 - - - +
78A ILE* 4.2 9.4 - - + -
79A VAL* 3.6 42.9 - - + +
116A LEU* 1.3 78.8 - - - +
118A GLU* 1.3 70.6 + - - +
119A GLY 5.0 0.2 - - - +
124A ILE* 3.5 31.4 - - + -
125A VAL 3.3 3.8 - - - +
126A LEU* 3.7 20.2 - - + -
227A TYR* 5.6 4.3 - - + +
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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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23A ASN* 2.8 32.7 + - - +
27A LYS* 2.8 43.2 + - + -
46A HIS* 3.3 25.3 - - - -
116A LEU* 4.1 10.1 - - + -
117A VAL* 1.3 83.1 - - - +
119A GLY* 1.3 58.2 + - - +
120A LYS* 4.2 11.2 + - - +
123A LYS 4.2 0.2 - - - +
124A ILE* 3.6 0.7 - - - -
125A VAL* 2.7 39.0 + - - +
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Residues in contact with GLY 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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117A VAL* 5.0 0.8 - - - +
118A GLU* 1.3 76.0 - - - +
120A LYS* 1.3 78.8 + - - +
121A GLY 3.9 2.2 + - - -
123A LYS 3.4 8.7 - - - -
124A ILE* 3.4 17.0 - - - -
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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