Contacts of the strand formed by residues 21 - 28 (chain K) 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 VAL 21 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11K TYR* 3.8 5.1 + - + +
18K THR* 3.2 33.9 + - + +
19K PHE 3.0 3.9 + - - +
20K GLY* 1.3 82.8 - - - +
22K SER* 1.3 71.1 + - - +
35K GLY 3.5 5.4 - - - +
36K ALA* 5.1 0.7 - - - -
37K GLY* 4.2 11.7 - - - +
277K LYS* 2.9 19.9 + - - -
308K ASP* 3.6 2.0 - - - -
344K LEU* 3.9 15.3 - - + -
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Residues in contact with SER 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K TYR* 3.4 5.8 - - - -
21K VAL* 1.3 86.4 - - - +
23K LYS* 1.3 66.3 + - - +
24K TYR 3.3 4.0 + - - -
25K PRO* 3.7 6.2 - - - +
35K GLY* 3.0 20.7 + - - +
277K LYS* 3.6 19.3 - - - -
281K GLY 3.4 10.5 + - - -
283K PRO* 3.3 33.2 - - - +
308K ASP* 3.7 5.2 - - - -
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Residues in contact with LYS 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H LYS* 3.4 47.4 + - - +
10K ALA* 2.8 40.8 + - + +
11K TYR* 3.6 19.8 + - + +
16K GLU* 5.8 2.2 - - - -
22K SER* 1.3 72.2 - - - +
24K TYR* 1.3 86.0 + - + +
25K PRO* 3.2 9.2 - - - +
281K GLY* 3.0 20.3 + - - +
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Residues in contact with TYR 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H LYS* 5.8 1.3 - - - -
19H ALA* 6.1 0.5 - - - +
10K ALA* 4.7 4.4 - - + +
22K SER* 4.1 3.6 - - - -
23K LYS* 1.3 110.8 + - + +
25K PRO* 1.3 68.2 - - - +
26K VAL* 3.7 3.3 - - - +
263K VAL 4.6 0.9 - - - +
280K THR 3.4 26.7 - - - -
281K GLY* 3.0 12.1 + - - +
282K MET* 4.6 14.6 - - + -
283K PRO* 3.4 18.2 - - - +
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Residues in contact with PRO 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K SER* 3.7 4.0 - - - +
23K LYS 3.2 14.1 - - - +
24K TYR* 1.3 91.0 - - - +
26K VAL* 1.3 61.7 + - - +
27K LYS* 4.4 2.7 - - + +
33K GLU* 5.0 7.9 - - - +
34K ILE 3.2 14.8 - - - +
35K GLY 3.6 20.6 - - - +
36K ALA* 4.4 12.8 - - + -
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Residues in contact with VAL 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K TYR 3.7 3.6 - - - +
25K PRO* 1.3 82.1 - - - +
27K LYS* 1.3 61.2 + - - +
33K GLU* 3.4 2.2 - - - -
34K ILE* 2.7 52.8 + - + +
213K ILE* 3.0 39.0 - - + -
263K VAL* 3.5 34.3 - - + +
264K GLY 3.7 14.1 - - - +
265K PRO* 5.0 0.2 - - + -
283K PRO* 3.6 16.6 - - + -
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Residues in contact with LYS 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E LYS* 6.1 6.5 - - - +
31E ASP* 2.3 49.2 + - - +
32E LEU 6.0 1.1 - - - -
33E GLU* 6.2 1.8 - - - -
119E LYS* 5.5 0.2 - - - +
25K PRO* 4.4 3.5 - - + +
26K VAL* 1.3 72.4 - - - +
28K ALA* 1.3 61.7 + - - +
32K LEU 3.5 5.8 - - - +
33K GLU* 3.1 37.4 + - + +
213K ILE* 3.0 17.2 - - - +
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Residues in contact with ALA 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K VAL 4.0 0.4 + - - -
27K LYS* 1.3 76.9 - - - +
29K GLY* 1.3 69.9 + - - +
31K ASP 4.0 0.3 + - - -
32K LEU* 3.0 33.6 + - + +
34K ILE* 4.8 8.7 - - + -
121K ALA* 4.5 5.2 - - + -
159K ASP* 4.4 7.0 - - + +
160K LEU* 3.9 19.3 - - + -
213K ILE* 3.5 18.2 - - + -
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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