Contacts of the strand formed by residues 119 - 126 (chain A) in PDB entry 2I2X
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU 3.5 10.8 - - - +
31A ASP* 3.5 40.7 + - + +
32A LEU* 3.7 15.9 - - + -
38A TYR* 3.8 24.9 - - + +
79A PRO* 3.2 20.9 + - + +
80A ALA* 3.2 8.1 - - + -
81A ILE 3.0 22.7 + - - -
113A HIS* 4.6 0.9 - - + -
117A GLY 4.4 5.4 - - - +
118A ILE* 1.3 72.9 - - - +
120A CYS* 1.3 62.9 + - - +
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Residues in contact with CYS 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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30A LEU* 2.9 55.0 + - - +
32A LEU* 4.1 7.1 - - - +
70A MET* 4.1 19.5 - - + -
81A ILE* 3.0 28.3 - - + +
83A LEU* 5.1 3.4 - - + -
106A LYS* 5.5 0.4 - - - -
109A MET* 4.2 16.6 - - - -
113A HIS* 4.6 0.4 - - - -
118A ILE 4.0 8.7 - - - -
119A LYS* 1.3 76.6 - - - +
121A ALA* 1.3 62.8 + - - +
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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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28A ALA* 4.5 5.2 - - + +
29A GLY* 4.2 8.5 - - - +
32A LEU* 3.6 23.3 - - + +
34A ILE* 5.6 0.2 - - + -
81A ILE 3.4 4.4 + - - -
82A ILE* 3.4 10.3 - - + +
83A LEU* 3.1 23.4 + - - +
106A LYS* 5.6 0.7 - - - +
109A MET* 4.5 6.6 - - - +
120A CYS* 1.3 76.2 - - - +
122A LEU* 1.3 60.3 - - - +
159A ASP* 3.5 18.8 - - + +
160A LEU* 4.7 10.1 - - + -
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Residues in contact with LEU 122 (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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83A LEU* 3.4 18.6 - - + +
85A THR* 4.1 2.2 - - - +
102A ALA* 3.8 20.9 - - - +
105A GLN* 3.9 26.5 - - + +
106A LYS* 4.4 4.5 - - + +
109A MET* 3.4 30.5 - - + -
121A ALA* 1.3 74.0 - - - +
123A ARG* 1.3 66.0 + - - +
124A HIS* 4.0 17.5 - - + +
157A GLY 3.7 21.5 - - - +
158A ALA* 3.8 2.4 - - - -
159A ASP* 2.7 45.2 + - - +
160A LEU* 3.0 7.5 + - - -
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Residues in contact with ARG 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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42A GLU* 2.8 54.8 + - - +
82A ILE* 4.5 1.3 - - + +
83A LEU 2.8 14.8 + - - +
84A GLU* 3.3 21.2 - - + -
85A THR 2.8 31.4 + - - -
121A ALA 4.2 0.6 + - - -
122A LEU* 1.3 73.7 - - - +
124A HIS* 1.3 63.5 + - - +
125A THR* 4.1 5.4 - - - +
160A LEU* 3.5 29.4 - - + +
162A SER* 3.2 27.0 + - - +
215A ALA* 3.8 5.6 - - - +
265A PRO* 2.5 38.4 + - - +
266A GLY* 3.4 14.9 + - - -
267A LYS* 3.4 10.6 - - - +
268A ASP 5.3 0.2 - - - +
285A THR* 3.5 10.5 + - - -
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Residues in contact with HIS 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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85A THR* 3.5 13.3 - - - +
87A HIS* 2.9 33.3 + + - +
91A MET* 4.4 0.4 - - - +
98A GLY 3.5 14.1 + - - -
101A VAL* 4.3 2.8 - - - +
102A ALA* 3.7 17.4 + - + +
105A GLN* 3.2 30.9 + - - -
122A LEU* 4.0 11.9 + - + +
123A ARG* 1.3 81.0 + - - +
125A THR* 1.3 60.8 + - - +
126A ILE* 3.9 10.1 + - + +
153A CYS* 3.5 17.3 - - + -
158A ALA* 3.7 17.2 - - + +
160A LEU 3.1 10.0 + - - +
161A LEU* 3.6 2.6 - - + -
162A SER 3.2 21.0 + - - +
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Residues in contact with THR 125 (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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84A GLU* 2.6 27.8 + - - +
85A THR 2.9 12.5 + - - -
86A GLU* 3.8 10.9 - - + -
87A HIS* 2.9 26.6 + - - +
123A ARG* 4.1 0.9 - - - +
124A HIS* 1.3 71.6 - - - +
126A ILE* 1.3 73.6 + - - +
162A SER* 3.3 16.4 - - - +
163A VAL* 3.9 17.3 - - - +
164A GLU* 4.1 10.5 - - + -
267A LYS* 4.1 19.3 - - - +
500B B13 5.9 1.8 - - - +
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Residues in contact with ILE 126 (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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87A HIS* 3.9 20.0 - - + +
92A SER* 3.8 10.3 - - - +
124A HIS* 4.0 18.4 - - + +
125A THR* 1.3 80.5 - - - +
127A GLY* 1.3 77.6 + - - +
146A PHE* 3.7 21.8 - - + -
149A ALA* 3.8 30.5 - - + +
150A PHE* 3.7 45.3 - - + +
153A CYS* 4.3 3.6 - - + -
161A LEU* 5.1 2.5 - - + -
162A SER 3.0 4.6 + - - -
163A VAL* 3.7 18.4 - - - +
164A GLU* 4.4 1.0 + - - +
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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