Contacts of the strand formed by residues 21 - 28 (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 VAL 21 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I TYR* 3.8 6.1 + - + +
18I THR* 3.2 39.3 + - + +
19I PHE 3.0 3.6 + - - +
20I GLY* 1.3 79.0 - - - +
22I SER* 1.3 70.7 + - - +
35I GLY 3.6 4.7 - - - +
36I ALA 5.3 0.2 - - - -
37I GLY* 4.5 9.0 - - - +
277I LYS* 3.2 16.1 + - - -
308I ASP* 3.8 2.2 - - - -
344I LEU* 4.2 11.9 - - + -
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Residues in contact with SER 22 (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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23A LYS 5.2 0.2 - - - +
11I TYR* 3.6 5.4 - - - -
21I VAL* 1.3 84.3 - - - +
23I LYS* 1.3 66.0 + - - +
24I TYR 3.6 0.4 + - - -
25I PRO* 3.9 8.8 - - - +
34I ILE 4.4 0.3 + - - -
35I GLY* 3.0 32.4 + - - +
277I LYS* 3.8 11.4 - - - -
281I GLY 3.4 13.2 - - - -
283I PRO* 3.4 26.1 - - - +
308I ASP* 3.3 8.9 + - - -
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Residues in contact with LYS 23 (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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22A SER 5.0 0.5 - - - +
23A LYS 3.8 3.1 - - - +
25A PRO* 3.4 18.4 - - + +
33A GLU* 5.4 0.2 + - - -
36A ALA* 2.7 37.0 + - - +
37A GLY* 4.8 2.0 - - - -
11D LYS* 5.6 3.8 - - - +
10I ALA* 3.3 35.3 + - + +
11I TYR* 3.7 14.8 + - + +
22I SER* 1.3 72.8 - - - +
24I TYR* 1.3 91.0 + - + +
25I PRO* 3.2 10.2 - - - +
281I GLY* 2.9 18.5 + - - +
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Residues in contact with TYR 24 (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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25A PRO* 3.6 40.2 - - + -
27A LYS* 3.5 34.3 - - + +
33A GLU* 2.6 32.1 + - - -
36A ALA* 3.8 3.0 - - + +
6I TYR* 6.4 0.4 - + - -
10I ALA* 4.6 4.7 - - + +
22I SER* 4.5 0.7 - - - -
23I LYS* 1.3 106.8 + - + +
25I PRO* 1.3 69.7 - - - +
26I VAL* 4.1 3.5 - - - +
263I VAL* 4.5 1.6 - - - +
280I THR 3.3 27.6 - - - -
281I GLY 2.9 12.2 + - - +
282I MET* 4.4 8.7 - - + -
283I PRO* 3.4 19.9 - - - +
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Residues in contact with PRO 25 (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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23A LYS* 3.3 26.2 - - + +
24A TYR* 3.9 29.9 - - + -
25A PRO* 4.1 5.4 - - + -
22I SER* 3.9 7.8 - - - +
23I LYS 3.2 11.4 - - - +
24I TYR* 1.3 89.4 - - - +
26I VAL* 1.3 61.4 + - - +
27I LYS* 4.4 1.7 + - - +
33I GLU* 5.8 0.4 - - + -
34I ILE 3.4 13.0 - - - +
35I GLY 3.8 20.4 - - - +
36I ALA* 4.2 6.7 - - + -
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Residues in contact with VAL 26 (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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24I TYR 4.1 1.6 - - - +
25I PRO* 1.3 78.6 - - - +
27I LYS* 1.3 66.9 + - - +
28I ALA* 4.0 1.2 + - + -
32I LEU 4.0 0.2 - - - +
33I GLU* 3.3 5.2 - - - -
34I ILE* 2.7 61.8 + - + +
213I ILE* 3.6 31.4 - - + -
263I VAL* 3.4 37.2 - - + +
264I GLY 3.8 14.8 - - - +
265I PRO* 4.7 0.4 - - + -
283I PRO* 3.9 9.2 - - + +
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Residues in contact with LYS 27 (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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6A TYR* 4.6 6.2 + - - -
24A TYR* 4.0 34.6 - - + +
280A THR 5.1 0.2 + - - -
282A MET* 3.7 28.1 - - - +
25I PRO 4.3 1.3 + - - +
26I VAL* 1.3 73.9 - - - +
28I ALA* 1.3 60.9 + - - +
32I LEU 3.6 4.5 - - - +
33I GLU* 3.1 37.5 - - + +
213I ILE* 3.0 18.4 - - - +
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Residues in contact with ALA 28 (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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26I VAL* 4.0 4.1 + - + -
27I LYS* 1.3 74.9 - - - +
29I GLY* 1.3 69.0 + - - +
32I LEU* 3.0 33.2 + - + +
34I ILE* 4.8 5.1 - - + +
121I ALA* 4.4 6.5 - - + -
159I ASP* 4.2 6.3 - - + +
160I LEU* 3.7 21.8 - - + -
213I ILE* 3.5 19.3 - - + -
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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