Contacts of the strand formed by residues 28 - 36 (chain K) in PDB entry 3IT8
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 GLN 28 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K HIS* 3.4 3.7 - - - -
25K TYR* 2.8 40.8 + - + +
26K ASN 3.2 0.2 - - - -
27K ASP* 1.3 103.7 - - - +
29K LEU* 1.3 65.8 + - - +
30K VAL* 3.3 2.1 + - - +
50K TRP* 4.2 20.3 - - + +
177K LYS 4.7 2.6 + - - -
178K ILE* 3.6 37.9 - - + +
179K PRO* 4.1 15.2 - - - +
208K TYR* 4.3 2.9 - - - +
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Residues in contact with LEU 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K TYR* 3.9 18.4 - - + -
23K ASP 3.6 6.3 - - - +
24K HIS* 3.4 27.6 + - + +
27K ASP 3.8 2.6 + - - -
28K GLN* 1.3 73.6 - - - +
30K VAL* 1.3 62.6 + - - +
31K THR 3.5 24.5 - - - +
32K LYS* 4.6 7.9 - - + -
46K PHE* 3.6 44.5 - - + -
48K ALA* 3.6 15.2 - - - +
50K TRP* 5.0 0.5 + - - -
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Residues in contact with VAL 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K ASP* 2.7 26.2 + - - +
25K TYR* 3.8 23.3 - - + +
28K GLN 3.5 14.1 - - - +
29K LEU* 1.3 75.0 - - - +
31K THR* 1.3 67.7 + - - +
46K PHE* 4.3 2.0 - - - -
47K ARG* 3.3 4.5 - - - -
48K ALA* 2.9 27.2 + - + -
50K TRP* 3.9 15.5 - - + -
51K PHE* 3.5 41.5 - - + -
170K TYR* 4.0 11.9 - - + -
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Residues in contact with THR 31 (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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21K PHE* 3.7 3.7 - - + +
22K TYR* 3.4 5.0 - - - -
23K ASP* 2.9 31.3 + - - -
29K LEU* 3.5 8.2 - - - +
30K VAL* 1.3 85.2 + - - +
32K LYS* 1.3 63.6 + - - +
33K ILE* 3.9 21.8 - - + -
44K VAL* 4.5 2.0 - - + -
46K PHE 3.3 9.6 - - - +
47K ARG* 2.3 41.4 + - - +
64K TYR* 3.0 29.6 + - + -
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Residues in contact with LYS 32 (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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20K VAL* 4.6 12.6 - - - -
21K PHE 3.3 4.5 - - - +
22K TYR* 3.7 41.1 + - + -
29K LEU* 4.6 6.5 - - + -
31K THR* 1.3 75.7 - - - +
33K ILE* 1.3 73.4 + - - +
34K SER* 5.0 1.3 - - - -
44K VAL* 3.5 2.9 - - - +
45K ASN* 2.8 50.4 + - + +
46K PHE* 3.1 25.7 + - + +
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Residues in contact with ILE 33 (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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20K VAL* 3.1 5.5 - - - +
21K PHE* 2.7 45.8 + - + +
31K THR* 3.9 12.1 - - + -
32K LYS* 1.3 80.4 - - - +
34K SER* 1.3 65.2 + - - +
42K GLY* 4.2 1.3 - - - -
43K ASN 3.2 22.2 - - - +
44K VAL* 3.9 12.3 - - + -
45K ASN* 3.7 2.5 - - - +
63K ASP* 3.6 38.6 - - + +
64K TYR* 3.8 17.7 - - + -
66K PHE* 3.6 31.9 - - + -
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Residues in contact with SER 34 (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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19K GLY 3.2 11.2 - - - -
20K VAL* 4.0 11.7 - - - -
32K LYS* 5.0 1.3 - - - -
33K ILE* 1.3 74.7 - - - +
35K TYR* 1.3 66.2 + - - +
36K ASN* 3.4 0.9 + - - -
42K GLY* 3.3 0.2 - - - -
43K ASN* 2.9 30.1 + - - +
45K ASN* 2.4 34.4 + - - -
66K PHE* 4.1 4.7 - - - -
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Residues in contact with TYR 35 (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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18K ASP* 4.7 3.3 - - - +
19K GLY 2.9 18.2 + - - +
34K SER* 1.3 72.2 - - - +
36K ASN* 1.3 67.0 + - - +
37K HIS* 3.5 41.9 + + - -
40K ARG* 3.2 54.6 + - - +
41K HIS* 3.5 14.1 - - - -
66K PHE* 3.8 9.3 - + + -
67K ASN* 5.4 2.2 - - + -
70K TYR* 3.4 65.1 - + + -
74K LYS* 5.9 0.5 + - - -
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Residues in contact with ASN 36 (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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34K SER 3.4 2.2 + - - -
35K TYR* 1.3 71.8 - - - +
37K HIS* 1.3 53.1 + - - +
38K GLU* 2.8 22.0 + - - +
39K THR* 2.6 43.6 + - - -
40K ARG* 2.6 36.7 + - - -
41K HIS 2.9 15.7 + - - +
43K ASN* 2.9 32.4 - - - +
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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