Contacts of the strand formed by residues 59 - 64 (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 ILE 59 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C TYR* 3.7 25.0 - - + +
57C HIS* 2.8 29.8 + - - -
24D ILE* 3.8 25.8 - - + -
25D TYR 3.7 10.3 - - - +
26D LEU* 4.3 0.9 - - + +
27D VAL* 3.9 1.6 - - - -
44D ILE* 3.7 31.2 - - + -
54D VAL* 3.7 23.3 - - + -
55D TYR 3.5 11.0 - - - +
56D LYS* 2.9 22.7 + - + +
58D ALA* 1.3 79.7 - - - +
60D SER* 1.3 62.3 + - - +
61D THR 3.8 11.9 - - - +
62D VAL* 4.2 2.7 - - + -
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Residues in contact with SER 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.3 15.7 - - - +
28C ASN* 4.7 3.2 + - - -
54C VAL* 3.5 3.5 - - - +
55C TYR* 3.0 27.2 + - - +
58C ALA* 3.5 20.9 - - - +
25D TYR* 2.7 34.3 + - - +
26D LEU 3.5 13.6 + - - -
27D VAL* 3.9 6.5 - - - +
59D ILE* 1.3 75.9 - - - +
61D THR* 1.3 78.8 + - - +
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Residues in contact with THR 61 (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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26C LEU* 4.3 5.4 - - + -
32C LEU* 3.8 19.0 - - + +
52C GLN* 3.4 30.2 + - - +
53C MET 3.2 7.6 - - - -
54C VAL* 3.9 10.1 - - + -
55C TYR* 5.2 0.2 - - - -
23D SER 4.0 0.3 - - - +
24D ILE* 3.5 2.9 - - - -
25D TYR* 2.8 55.5 + - + +
59D ILE* 3.9 2.3 - - - +
60D SER* 1.3 97.0 + - - +
62D VAL* 1.3 66.0 + - - +
63D VAL* 3.8 1.7 - - - +
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Residues in contact with VAL 62 (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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52C GLN* 3.6 4.3 - - - -
53C MET* 3.0 57.1 + - + +
55C TYR* 4.4 3.4 - - + -
11D TYR* 3.9 3.6 + - + -
12D LEU* 4.8 9.6 - - + -
15D LEU* 3.9 27.8 - - + -
22D VAL* 4.5 12.1 - - + -
23D SER 3.5 7.0 - - - +
24D ILE* 4.6 13.7 - - + -
36D ILE* 5.3 2.5 - - + -
44D ILE* 5.0 5.6 - - + -
59D ILE* 4.2 15.0 - - + -
61D THR* 1.3 77.1 - - - +
63D VAL* 1.3 64.2 + - - +
64D PRO* 3.6 3.6 - - - +
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Residues in contact with VAL 63 (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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50C VAL* 5.3 7.2 - - + +
52C GLN* 3.8 37.0 - - + +
22D VAL* 4.4 1.8 - - - -
23D SER* 2.8 41.2 + - - +
25D TYR* 3.8 27.4 - - + +
61D THR* 3.8 3.8 - - - +
62D VAL* 1.3 76.5 - - - +
64D PRO* 1.3 75.8 - - + +
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Residues in contact with PRO 64 (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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50C VAL* 4.0 16.0 - - + +
51C SER 3.7 12.8 - - - +
11D TYR* 3.1 30.3 - - + +
15D LEU* 3.7 28.9 - - + -
20D VAL* 4.3 2.0 - - + -
21D PRO 3.8 5.8 - - - +
22D VAL* 3.9 4.7 - - + -
62D VAL 3.6 2.7 - - - +
63D VAL* 1.3 98.6 - - + +
65D SER* 1.3 62.1 + - - +
66D ARG 3.2 20.8 + - - +
68D VAL* 4.3 8.1 - - + -
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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