Contacts of the strand formed by residues 23 - 31 (chain H) in PDB entry 1U3H
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 ARG 23 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G ILE* 4.7 7.9 - - - +
2G GLU* 3.7 27.2 + - - +
16H TYR 3.9 0.8 - - - +
17H PHE* 3.9 0.2 - - - -
18H THR* 3.1 62.1 + - + +
21H THR 4.2 0.9 - - - -
22H GLN* 1.3 80.7 - - + +
24H ILE* 1.3 71.9 + - - +
25H ARG* 4.5 33.4 - - - +
43H ASP* 4.7 7.7 + - - -
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Residues in contact with ILE 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H TYR 3.4 7.2 - - - +
17H PHE* 4.0 21.5 - - + -
21H THR* 3.4 32.8 - - - +
22H GLN 3.7 2.5 + - - +
23H ARG* 1.3 85.4 - - - +
25H ARG* 1.3 66.3 + - - +
42H SER* 3.9 1.7 + - - -
43H ASP* 5.3 0.9 - - - +
75H LEU* 3.6 40.4 - - + +
79H CYS* 4.2 15.3 - - + -
80H ARG* 3.7 36.3 - - + +
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Residues in contact with ARG 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ILE* 3.2 47.0 - - - +
15H CYS* 3.8 0.5 - - - -
16H TYR* 2.8 53.1 + - + +
23H ARG* 4.5 20.4 - - - +
24H ILE* 1.3 75.0 - - - +
26H TYR* 1.3 62.6 + - - +
27H VAL* 4.1 8.5 - - + +
41H ASP* 2.7 38.2 + - - +
42H SER* 3.4 11.2 - - - +
43H ASP* 3.6 32.1 + - - +
44H VAL* 6.0 0.6 - - - +
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Residues in contact with TYR 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H PHE* 5.4 0.3 - - - -
13H PRO* 4.7 1.6 - - + -
14H PHE 3.2 17.9 - - - -
15H CYS* 4.4 1.3 - - - -
24H ILE 4.0 0.4 + - - -
25H ARG* 1.3 73.4 - - - +
27H VAL* 1.3 63.2 + - - +
28H THR* 3.6 17.9 + - - -
40H PHE* 3.8 15.5 - + - -
41H ASP* 3.7 1.0 - - - -
42H SER* 2.9 37.4 + - - -
71H THR* 3.3 38.4 - - + -
74H GLU* 2.7 28.7 + - + -
75H LEU* 3.8 31.9 - - + -
78H VAL* 5.6 0.4 - - + -
79H CYS* 3.4 23.1 - - - -
2I SER* 3.0 33.7 + - - -
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Residues in contact with VAL 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ILE* 4.9 5.8 - - + -
12H GLN 3.9 1.1 - - - +
13H PRO* 3.6 1.6 - - - +
14H PHE* 2.8 40.9 + - + +
16H TYR* 3.9 24.9 - - + -
25H ARG* 4.0 12.3 + - + +
26H TYR* 1.3 82.6 - - - +
28H THR* 1.3 64.9 + - - +
29H ARG* 4.0 35.0 - - + +
39H ARG* 4.1 12.3 - - + -
40H PHE* 3.3 9.9 - - - +
41H ASP* 3.9 21.5 - - - +
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Residues in contact with THR 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H PHE* 3.6 18.5 - - + -
12H GLN 4.1 2.7 - - - -
13H PRO* 4.5 2.3 - - - +
26H TYR* 3.6 22.5 + - - -
27H VAL* 1.3 74.9 + - - +
29H ARG* 1.3 60.6 + - - +
30H TYR* 2.9 37.0 - - + +
39H ARG* 3.2 8.5 - - - +
40H PHE* 2.9 43.9 + - + +
47H TYR* 4.1 14.8 - - + +
71H THR* 4.7 3.0 - - - +
74H GLU* 5.2 0.2 + - - -
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Residues in contact with ARG 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G ILE* 3.9 25.5 - - - +
143G TYR* 3.4 31.1 + - - -
10H GLN 3.5 2.1 - - - +
11H PHE* 3.6 4.2 - - - -
12H GLN* 3.1 36.5 + - + +
14H PHE* 3.7 27.4 - - - -
16H TYR* 4.0 9.9 + - - -
27H VAL* 4.0 17.2 - - + +
28H THR* 1.3 76.9 - - - +
30H TYR* 1.3 63.1 + - - +
31H ILE* 3.5 17.5 - - + +
36H GLU* 2.9 33.3 + - - +
38H LEU 4.0 3.4 - - - -
39H ARG* 3.5 17.8 - - - +
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Residues in contact with TYR 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ASN* 4.7 0.2 - - - -
10H GLN 3.8 2.9 - - - -
11H PHE* 3.5 13.9 - + - -
28H THR* 2.9 29.2 - - + +
29H ARG* 1.3 75.6 - - - +
31H ILE* 1.3 55.0 + - - +
36H GLU* 3.3 2.8 - - - -
37H TYR* 2.7 64.4 + + + -
38H LEU* 3.0 30.5 + - + +
39H ARG 4.7 0.4 - - - -
47H TYR* 3.8 11.7 + + - -
61H TYR* 3.8 19.3 - + - -
3I GLN 3.9 1.0 + - - -
4I TYR* 3.5 31.9 - + - -
5I ARG* 3.0 45.6 + - - +
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Residues in contact with ILE 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G TYR* 4.1 26.0 - - + -
9H VAL* 3.5 5.0 - - - +
10H GLN* 2.9 59.4 + - + +
12H GLN* 4.5 7.0 - - + -
29H ARG* 3.5 32.1 - - + +
30H TYR* 1.3 79.8 - - - +
32H TYR* 1.3 63.6 + - - +
33H ASN 3.7 17.0 - - - +
34H ARG 3.9 2.9 - - - -
35H GLU 3.0 23.3 - - - +
36H GLU* 3.8 15.9 - - + -
37H TYR* 3.6 8.3 + - - -
4I TYR* 4.8 0.9 + - - -
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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
------------------------------------------------------------
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