Contacts of the strand formed by residues 119 - 126 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I LEU 3.6 5.8 - - - +
31I ASP* 3.2 44.8 + - + +
32I LEU* 3.9 13.0 - - + -
38I TYR* 3.8 26.2 - - + +
79I PRO* 3.0 21.3 + - + +
80I ALA* 3.1 6.6 - - + +
81I ILE 3.0 23.9 + - - -
113I HIS* 4.6 0.2 - - - -
117I GLY 3.3 8.7 + - - +
118I ILE* 1.3 70.9 - - - +
120I CYS* 1.3 62.6 + - - +
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Residues in contact with CYS 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I LEU* 2.7 55.9 + - - +
32I LEU* 3.9 8.3 - - - +
70I MET* 3.8 22.2 - - + -
81I ILE* 3.0 28.3 - - + +
83I LEU* 5.5 0.7 - - + -
106I LYS* 6.1 0.4 - - - -
109I MET* 4.0 26.7 - - - -
118I ILE 4.0 9.2 - - - -
119I LYS* 1.3 75.9 - - - +
121I ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I ALA* 4.4 6.1 - - + +
29I GLY* 4.1 12.1 - - - +
32I LEU* 3.6 21.5 - - + +
81I ILE 3.4 3.9 + - - +
82I ILE* 3.3 10.3 - - + +
83I LEU* 3.1 23.4 + - - +
106I LYS* 5.4 0.9 - - - +
109I MET* 4.6 7.2 - - - +
120I CYS* 1.3 79.4 - - - +
122I LEU* 1.3 62.3 + - - +
159I ASP* 3.3 18.4 - - + +
160I LEU* 4.9 7.6 - - + -
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Residues in contact with LEU 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I ILE* 5.0 0.2 - - - -
83I LEU* 3.4 18.6 - - + +
85I THR* 4.0 8.1 - - - +
102I ALA* 3.6 24.7 - - - +
105I GLN* 3.8 23.1 - - + +
106I LYS* 4.2 3.6 - - + +
109I MET* 3.6 34.8 - - + -
121I ALA* 1.3 74.6 - - - +
123I ARG* 1.3 61.7 + - - +
124I HIS* 3.9 19.5 - - + +
157I GLY 3.9 17.3 - - - +
158I ALA* 3.8 2.4 - - - -
159I ASP* 2.6 42.5 + - - +
160I LEU* 2.8 9.8 + - - -
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Residues in contact with ARG 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I GLU* 2.8 46.9 + - - +
82I ILE* 4.6 1.7 - - + +
83I LEU 2.8 11.5 + - - +
84I GLU* 3.2 16.8 + - + -
85I THR* 2.9 26.5 + - - -
121I ALA 4.3 0.2 - - - -
122I LEU* 1.3 75.5 - - - +
124I HIS* 1.3 67.0 + - - +
125I THR* 4.0 10.3 - - - +
160I LEU* 3.3 25.9 - - + +
162I SER* 3.0 28.1 + - - +
215I ALA* 3.7 5.9 - - - +
216I GLY 4.6 0.4 - - - +
265I PRO* 2.4 41.1 + - - +
266I GLY 3.2 15.6 + - - -
267I LYS* 3.4 10.2 - - - +
268I ASP 4.9 0.2 - - - +
285I THR* 3.2 13.1 + - - -
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Residues in contact with HIS 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I THR* 3.5 15.1 - - - +
87I HIS* 2.9 32.4 + + - +
98I GLY 3.5 13.6 + - - -
101I VAL* 4.1 2.6 - - - +
102I ALA* 3.5 19.2 + - + +
105I GLN* 3.2 30.2 + - - -
122I LEU* 3.9 11.8 - - + +
123I ARG* 1.3 78.9 + - - +
125I THR* 1.3 61.4 + - - +
126I ILE* 3.7 7.5 - - + +
153I CYS* 3.5 22.2 - - + -
158I ALA* 3.9 17.5 - - + +
160I LEU 2.9 10.1 + - - +
161I LEU* 3.7 3.1 - - + -
162I SER 3.1 22.9 + - - +
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Residues in contact with THR 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I GLU* 2.6 28.3 + - - +
85I THR 3.0 12.3 + - - -
86I GLU* 3.7 9.3 - - + -
87I HIS* 2.9 27.1 + - - -
123I ARG* 4.0 1.7 - - - +
124I HIS* 1.3 71.7 - - - +
126I ILE* 1.3 64.1 + - - +
127I GLY* 3.7 0.3 + - - -
162I SER* 3.2 17.8 - - - +
163I VAL* 3.7 26.9 - - - +
164I GLU* 4.2 7.2 - - + -
267I LYS* 3.8 17.4 - - - +
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Residues in contact with ILE 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I HIS* 3.9 22.2 - - + +
92I SER* 3.6 13.2 - - - +
124I HIS* 3.7 22.7 - - + +
125I THR* 1.3 76.9 - - - +
127I GLY* 1.3 75.7 + - - +
146I PHE* 3.9 23.8 - - + -
149I ALA* 4.0 12.1 - - + +
150I PHE* 3.7 53.8 - - + +
153I CYS* 4.6 3.6 - - + -
161I LEU* 4.7 2.2 - - + -
162I SER 3.1 3.2 + - - -
163I VAL* 3.3 20.4 - - - +
164I 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