Contacts of the strand formed by residues 119 - 126 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30O LEU 3.4 9.4 - - - +
31O ASP* 3.2 43.4 + - + +
32O LEU* 3.8 15.9 - - + -
33O GLU* 6.2 0.4 - - - -
38O TYR* 3.8 26.0 - - + +
79O PRO* 3.2 21.0 + - + +
80O ALA* 3.1 7.1 - - + -
81O ILE 3.0 23.0 + - - -
113O HIS* 4.5 0.2 - - - -
117O GLY 4.4 6.8 + - - +
118O ILE* 1.3 74.1 - - - +
120O CYS* 1.3 63.8 + - - +
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Residues in contact with CYS 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O GLY* 3.7 0.2 - - - -
30O LEU* 2.6 62.7 + - - +
32O LEU* 3.9 9.3 - - - +
70O MET* 4.1 19.1 - - + -
81O ILE* 3.0 29.8 - - + +
83O LEU* 5.3 0.7 - - + -
109O MET* 4.3 19.7 - - - -
113O HIS* 4.7 0.4 - - - -
118O ILE 4.1 9.9 - - - -
119O LYS* 1.3 75.6 - - - +
121O ALA* 1.3 61.7 + - - +
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Residues in contact with ALA 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O ALA* 4.6 2.9 - - + +
29O GLY* 4.0 11.0 - - - +
32O LEU* 3.6 21.3 - - + -
34O ILE* 5.7 0.2 - - + -
81O ILE 3.5 3.1 + - - +
82O ILE* 3.4 9.6 - - + +
83O LEU* 3.2 22.7 + - - +
106O LYS* 5.2 1.3 - - - +
109O MET* 4.5 7.5 - - - +
120O CYS* 1.3 78.3 - - - +
122O LEU* 1.3 61.4 + - - +
159O ASP* 3.3 19.3 - - + +
160O LEU* 4.9 10.1 - - + -
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Residues in contact with LEU 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O ILE* 5.0 0.2 - - - -
83O LEU 3.6 11.2 - - - +
85O THR* 3.9 3.4 - - - +
102O ALA* 3.5 37.5 - - - +
105O GLN* 3.6 23.6 - - + +
106O LYS* 4.4 4.3 - - + +
109O MET* 4.0 22.9 - - + -
121O ALA* 1.3 73.8 - - - +
123O ARG* 1.3 68.7 + - - +
124O HIS* 3.6 21.8 - - + +
157O GLY 3.6 19.5 - - - +
158O ALA* 4.0 2.0 - - - -
159O ASP* 2.8 41.1 + - - +
160O LEU* 3.0 10.0 + - - +
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Residues in contact with ARG 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O GLU* 2.7 47.5 + - - +
82O ILE* 4.5 1.3 - - + +
83O LEU 2.8 12.9 + - - +
84O GLU* 3.5 19.9 - - + -
85O THR 2.8 27.0 + - - -
121O ALA 4.2 0.2 - - - -
122O LEU* 1.3 74.0 - - - +
124O HIS* 1.3 70.5 + - - +
125O THR* 4.1 6.1 - - - +
160O LEU* 3.5 24.5 - - + +
162O SER* 3.1 27.2 + - - +
215O ALA* 3.7 6.9 - - - +
216O GLY 4.6 0.2 - - - +
265O PRO* 2.5 40.1 + - - +
266O GLY* 3.3 15.3 + - - -
267O LYS* 3.4 11.1 - - - +
285O THR* 3.4 12.9 + - - -
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Residues in contact with HIS 124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85O THR* 3.5 14.9 - - - +
87O HIS* 2.9 32.2 + + - +
91O MET* 4.5 0.4 - - - +
98O GLY 3.7 6.6 + - - -
101O VAL* 4.1 3.2 - - - +
102O ALA* 3.5 24.4 + - + +
105O GLN* 3.0 31.4 + - - -
122O LEU* 3.6 13.5 + - + +
123O ARG* 1.3 79.8 + - - +
125O THR* 1.3 61.4 + - - +
126O ILE* 3.6 14.0 - - + +
153O CYS* 3.6 16.2 - - + -
158O ALA* 3.9 16.5 - - + +
160O LEU 3.0 10.6 + - - +
161O LEU* 3.7 1.6 - - + -
162O SER 3.0 22.5 + - - -
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Residues in contact with THR 125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84O GLU* 2.7 28.1 + - - +
85O THR 3.1 7.3 + - - -
86O GLU* 3.7 15.5 - - + +
87O HIS* 3.0 27.4 + - - +
123O ARG* 4.1 1.4 - - - +
124O HIS* 1.3 74.4 - - - +
126O ILE* 1.3 64.4 + - - +
162O SER* 3.3 15.4 - - - -
163O VAL* 3.7 26.0 - - - +
164O GLU* 4.2 7.0 - - + -
267O LYS* 3.9 19.1 - - - -
500P B13 6.1 0.7 - - - +
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Residues in contact with ILE 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O HIS* 4.1 11.2 - - + +
92O SER* 3.4 13.9 - - - +
124O HIS* 3.6 28.5 - - + +
125O THR* 1.3 78.8 - - - +
127O GLY* 1.3 77.5 + - - +
146O PHE* 4.2 17.3 - - + +
149O ALA* 3.7 18.8 - - + -
150O PHE* 3.7 55.0 - - + +
153O CYS* 4.8 3.6 - - - -
161O LEU* 4.8 3.6 - - + -
162O SER 2.9 3.6 + - - -
163O VAL* 3.3 21.0 - - - +
164O GLU 4.4 0.9 + - - -
500P B13 5.6 0.2 - - - +
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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