Contacts of the strand formed by residues 119 - 126 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G LEU 3.5 6.1 - - - +
31G ASP* 3.2 43.9 + - + +
32G LEU* 3.7 15.9 - - + -
33G GLU* 6.4 0.4 - - - -
38G TYR* 4.0 25.4 - - + +
79G PRO* 2.9 23.6 + - + +
80G ALA* 3.0 7.4 - - + -
81G ILE 2.9 23.6 + - - -
113G HIS* 4.6 0.4 - - - -
117G GLY 4.3 9.1 + - - +
118G ILE* 1.3 72.4 - - - +
120G CYS* 1.3 63.8 + - - +
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Residues in contact with CYS 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G GLY 3.8 0.3 - - - -
30G LEU* 2.9 59.0 + - - +
32G LEU* 4.0 9.0 - - - +
70G MET* 4.1 22.0 - - + -
81G ILE* 3.0 28.3 - - + +
83G LEU* 5.3 0.4 - - + -
109G MET* 4.1 16.2 - - - -
118G ILE 4.1 8.5 - - - +
119G LYS* 1.3 75.8 - - - +
121G ALA* 1.3 62.6 + - - +
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Residues in contact with ALA 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G ALA* 4.4 5.6 - - + +
29G GLY* 4.0 13.0 - - - +
32G LEU* 3.9 19.5 - - + +
34G ILE* 5.8 0.2 - - + -
81G ILE 3.3 4.7 + - - +
82G ILE* 3.4 9.8 - - + +
83G LEU* 3.0 25.6 + - - +
106G LYS* 5.6 1.1 - - - +
109G MET* 4.6 6.1 - - - +
120G CYS* 1.3 77.6 - - - +
122G LEU* 1.3 63.2 + - - +
123G ARG 4.1 0.4 - - - -
159G ASP* 3.4 18.6 - - + +
160G LEU* 5.0 7.0 - - + -
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Residues in contact with LEU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G LEU* 3.4 17.5 - - + +
85G THR* 3.8 3.8 - - - +
102G ALA* 3.7 21.5 - - - +
105G GLN* 3.6 32.8 - - + +
106G LYS* 4.1 4.0 - - + +
109G MET* 3.6 25.1 - - + -
121G ALA* 1.3 74.4 - - - +
123G ARG* 1.3 68.3 + - - +
124G HIS* 3.8 17.5 - - + +
157G GLY 3.6 22.4 - - - +
158G ALA* 3.6 1.1 - - - -
159G ASP* 2.6 45.1 + - - +
160G LEU* 3.0 7.6 + - - -
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Residues in contact with ARG 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G GLU* 2.8 49.3 + - - +
82G ILE* 4.6 1.3 - - + +
83G LEU 2.7 14.4 + - - +
84G GLU* 3.7 18.4 - - - -
85G THR 2.9 25.6 + - - -
121G ALA 4.1 0.6 + - - -
122G LEU* 1.3 74.4 - - - +
124G HIS* 1.3 69.2 + - - +
125G THR* 3.8 8.7 - - - +
160G LEU* 3.4 31.4 - - + +
162G SER* 3.1 27.5 + - - +
215G ALA* 3.8 5.2 - - - +
265G PRO* 2.4 40.9 + - - +
266G GLY 3.3 16.5 - - - -
267G LYS* 3.5 9.7 - - - +
268G ASP 5.4 0.2 - - - -
285G THR* 3.6 7.5 + - - -
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Residues in contact with HIS 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G THR* 3.4 15.8 - - - +
87G HIS* 3.1 29.6 - + - +
98G GLY* 3.5 8.4 + - - -
101G VAL* 4.1 3.2 - - - +
102G ALA* 3.4 27.9 + - + +
105G GLN* 3.0 31.3 + - - -
122G LEU* 3.8 11.0 + - + +
123G ARG* 1.3 82.3 + - - +
125G THR* 1.3 61.8 + - - +
126G ILE* 3.8 11.8 + - + +
153G CYS* 3.6 16.2 - - + -
158G ALA* 3.8 16.2 - - + +
160G LEU 3.1 9.9 + - - +
161G LEU* 3.7 2.7 - - + -
162G SER 3.2 21.3 + - - +
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Residues in contact with THR 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G GLU* 2.6 33.6 + - - +
85G THR 2.8 13.2 + - - -
86G GLU* 3.8 9.4 - - + +
87G HIS* 3.1 23.9 + - - -
123G ARG* 3.8 2.3 - - - -
124G HIS* 1.3 72.9 - - - +
126G ILE* 1.3 63.4 + - - +
127G GLY* 3.6 0.5 + - - -
162G SER* 3.2 25.5 - - - +
163G VAL* 3.8 11.7 - - - +
164G GLU* 4.3 5.8 - - + +
267G LYS* 3.7 21.3 - - + +
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Residues in contact with ILE 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G HIS* 3.6 30.3 - - + +
92G SER* 3.6 8.5 - - - +
124G HIS* 3.9 20.2 - - + +
125G THR* 1.3 74.5 - - - +
127G GLY* 1.3 74.9 + - - +
146G PHE* 4.1 10.3 - - + -
149G ALA* 3.7 25.8 - - + -
150G PHE* 3.9 48.5 - - + +
153G CYS* 4.2 9.2 - - + -
161G LEU* 5.1 1.8 - - + -
162G SER 2.9 6.1 + - - -
163G VAL* 3.4 22.2 - - - +
164G GLU 4.2 1.6 + - - -
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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