Contacts of the strand formed by residues 31 - 39 (chain D) in PDB entry 1U1T
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 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D SER* 4.3 9.6 + - - +
24D ILE 3.7 3.4 - - - +
25D TYR* 3.0 48.3 + - + -
29D GLY 3.5 2.7 + - - +
30D ILE* 1.3 76.1 - - - +
32D LEU* 1.3 75.5 + - - +
33D GLN* 3.7 28.9 + - + +
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D SER* 3.2 5.4 - - - -
24D ILE* 2.7 43.1 + - + +
26D LEU* 4.0 22.4 - - + -
30D ILE* 4.1 13.5 - - + -
31D LYS* 1.3 79.8 - - - +
33D GLN* 1.3 63.4 + - - +
46D LEU* 3.6 19.1 - - + -
52D GLN* 4.2 16.8 - - - +
54D VAL* 3.8 29.6 - - + -
61E THR* 4.0 14.8 - - + -
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Residues in contact with GLN 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D VAL 3.4 6.1 - - - +
23D SER* 3.6 19.6 + - - +
31D LYS* 3.7 25.9 + - + +
32D LEU* 1.3 80.1 - - - +
34D GLY* 1.3 59.2 + - - +
46D LEU* 4.2 9.1 - - - +
48D ASN* 2.8 34.7 + - - +
52D GLN* 5.7 0.3 + - - -
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Residues in contact with GLY 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PRO* 3.4 7.3 - - - +
22D VAL* 2.8 30.6 + - - -
33D GLN* 1.3 76.5 - - - +
35D GLN* 1.3 59.9 + - - -
46D LEU* 4.0 7.3 - - - +
47D LYS 3.1 13.9 - - - -
48D ASN* 3.6 8.3 - - - -
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Residues in contact with GLN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG 5.3 0.4 + - - -
19D ARG* 3.6 51.3 - - - +
20D VAL 3.9 16.2 - - - +
21D PRO* 4.8 1.3 - - + -
22D VAL* 4.4 2.2 - - - -
34D GLY* 1.3 74.6 - - - +
36D ILE* 1.3 69.3 + - - +
37D GLU* 3.3 3.2 + - - +
46D LEU* 3.5 9.4 - - - +
47D LYS* 3.0 65.5 + - + +
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Residues in contact with ILE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.4 14.6 - - + +
15D LEU* 4.3 22.1 + - + +
16D ARG* 3.5 34.1 - - + +
19D ARG* 5.7 0.2 - - - -
20D VAL 4.7 2.0 + - - -
22D VAL* 4.1 14.4 - - + -
24D ILE* 3.9 21.1 - - + -
35D GLN* 1.3 77.6 + - - +
37D GLU* 1.3 63.7 + - - +
38D SER 3.9 12.1 - - - +
39D PHE* 4.1 17.5 - - + -
44D ILE* 3.4 38.6 - - + -
45D LEU 3.8 2.2 - - - -
46D LEU* 4.3 1.6 - - + -
62D VAL* 5.3 2.5 - - + -
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Residues in contact with GLU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG* 3.4 16.8 + - - +
35D GLN* 3.3 6.1 + - + +
36D ILE* 1.3 74.2 - - - +
38D SER* 1.3 63.7 + - - +
45D LEU* 2.8 42.7 + - + +
47D LYS* 3.3 38.7 - - + +
51D SER* 4.7 5.7 + - - -
70E LEU* 5.4 4.2 - - - +
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Residues in contact with SER 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG* 4.0 12.8 - - - +
36D ILE* 3.5 1.0 - - - +
37D GLU* 1.3 80.5 - - - +
39D PHE* 1.3 69.4 + - - +
44D ILE* 3.6 3.5 - - - +
45D LEU* 2.7 47.2 + - - +
3E LYS* 6.2 0.4 - - - -
7E LEU* 3.4 20.6 - - - +
70E LEU* 5.3 0.5 - - - +
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Residues in contact with PHE 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ASP* 3.7 42.0 - - + -
12D LEU* 3.6 35.2 - - + -
13D ASN* 3.7 22.7 - - + -
16D ARG* 4.5 5.4 - - - -
36D ILE* 4.1 9.6 - - + -
38D SER* 1.3 85.9 - - - +
40D ASP* 1.3 74.0 + - - +
43D VAL 3.3 15.9 - - - +
44D ILE* 4.0 13.5 - - + -
56D LYS* 4.5 1.6 - - - -
3E LYS* 3.2 47.2 - - + +
6E SER* 4.6 1.2 + - - -
7E LEU* 3.7 10.2 - - - +
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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