Contacts of the strand formed by residues 119 - 126 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C LEU 3.5 6.5 - - - +
31C ASP* 2.8 52.8 + - + +
32C LEU* 3.9 16.2 - - + -
38C TYR* 4.0 24.2 - - + +
79C PRO* 3.0 24.3 + - + +
80C ALA* 3.2 5.4 - - + -
81C ILE 2.9 24.1 + - - -
113C HIS* 4.5 0.4 - - - -
117C GLY 4.4 7.4 + - - +
118C ILE* 1.3 72.4 - - - +
120C CYS* 1.3 62.8 + - - +
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Residues in contact with CYS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY* 3.7 0.2 - - - -
30C LEU* 2.8 61.6 + - - +
32C LEU* 4.1 9.7 - - - +
70C MET* 3.9 22.9 - - + -
81C ILE* 3.0 29.6 - - + +
83C LEU* 5.4 0.7 - - + -
109C MET* 4.2 17.7 - - - -
118C ILE 4.0 7.4 - - - -
119C LYS* 1.3 76.0 - - - +
121C ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ALA* 4.5 5.6 - - + +
29C GLY* 3.9 13.0 - - - +
32C LEU* 3.8 19.5 - - + +
34C ILE* 5.4 0.4 - - + -
81C ILE 3.3 3.9 + - - +
82C ILE* 3.3 10.4 - - + +
83C LEU* 3.1 24.3 + - - +
106C LYS* 5.3 1.3 - - - +
109C MET* 4.6 7.1 - - - +
120C CYS* 1.3 77.3 - - - +
122C LEU* 1.3 61.4 - - - +
159C ASP* 3.4 18.6 - - + +
160C LEU* 4.8 9.2 - - + -
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 3.4 17.7 - - + +
85C THR* 3.9 4.0 - - - +
102C ALA* 3.8 22.7 - - - +
105C GLN* 3.7 21.8 - - + +
106C LYS* 4.3 4.5 - - + +
109C MET* 3.5 35.4 - - + -
121C ALA* 1.3 74.8 - - - +
123C ARG* 1.3 65.5 + - - +
124C HIS* 3.9 19.1 - - + +
157C GLY 3.9 14.8 - - - +
158C ALA* 3.8 5.6 - - - -
159C ASP* 2.7 41.8 + - - +
160C LEU* 3.0 9.8 + - - -
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Residues in contact with ARG 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLU* 2.8 54.7 + - - +
82C ILE* 4.6 0.6 - - + +
83C LEU 2.8 12.6 + - - +
84C GLU* 3.3 18.4 + - + -
85C THR 2.8 26.3 + - - -
121C ALA 4.3 0.2 - - - -
122C LEU* 1.3 74.1 - - - +
124C HIS* 1.3 69.2 + - - +
125C THR* 3.9 11.2 - - - +
160C LEU* 3.4 25.0 - - + +
162C SER* 3.0 27.6 + - - +
215C ALA* 3.6 7.7 - - - +
216C GLY 4.7 0.4 - - - +
265C PRO* 2.5 39.3 + - - +
266C GLY 3.3 14.6 + - - -
267C LYS* 3.7 8.9 - - - +
268C ASP 5.1 0.4 - - - +
285C THR* 3.4 11.9 + - - -
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Residues in contact with HIS 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C THR* 3.5 14.8 - - + +
87C HIS* 2.9 32.5 + + - +
91C MET* 4.5 0.4 - - - +
98C GLY 3.5 15.1 + - - -
101C VAL* 4.1 3.0 - - - +
102C ALA* 3.7 18.7 + - + +
105C GLN* 3.2 30.3 + - - -
122C LEU* 3.9 11.9 + - + +
123C ARG* 1.3 82.0 + - - +
125C THR* 1.3 59.8 - - - +
126C ILE* 3.8 10.9 - - + +
153C CYS* 3.7 15.3 - - + -
158C ALA* 3.8 17.1 - - + +
160C LEU 3.0 9.5 + - - +
161C LEU* 3.6 3.4 - - + -
162C SER 3.2 21.3 + - - +
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Residues in contact with THR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLU* 2.6 27.9 + - - +
85C THR 3.0 11.8 + - - -
86C GLU* 3.8 8.9 - - + +
87C HIS* 3.0 26.8 + - - +
123C ARG* 3.9 1.7 - - - +
124C HIS* 1.3 72.2 - - - +
126C ILE* 1.3 63.7 + - - +
162C SER* 3.3 23.1 - - - +
163C VAL* 3.9 14.4 - - - -
164C GLU* 4.1 10.5 - - + +
267C LYS* 3.7 21.8 - - - +
500D B13 6.0 0.9 - - - +
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Residues in contact with ILE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C HIS* 4.1 13.0 - - + -
92C SER* 3.6 11.9 - - - +
124C HIS* 3.8 25.8 - - + +
125C THR* 1.3 76.9 - - - +
127C GLY* 1.3 76.1 + - - +
128C ASP 3.7 0.2 + - - -
146C PHE* 4.0 7.6 - - + -
149C ALA* 3.9 30.5 - - + +
150C PHE* 3.7 57.0 - - + +
153C CYS* 4.5 4.3 - - + -
161C LEU* 4.7 3.1 - - + -
162C SER 3.1 3.6 + - - -
163C VAL* 3.4 20.1 - - - +
164C GLU* 4.4 1.2 + - - +
500D B13 5.5 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