Contacts of the strand formed by residues 20 - 24 (chain D) in PDB entry 1UUG
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 GLU 20 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C TYR* 4.1 18.0 + - + -
67C HIS* 4.8 4.0 - - - -
86C PRO* 3.8 7.5 - - + +
87C PRO* 3.7 19.4 - - + +
88C SER* 2.8 50.3 + - - -
189C SER* 4.4 1.0 + - - -
190C PRO* 4.1 7.8 - - - +
18D ILE* 3.6 4.8 - - - +
19D GLN* 1.3 79.5 - - - +
21D SER* 1.3 67.5 + - - +
22D ILE* 4.1 18.7 - - + +
43D VAL 3.7 0.6 - - - +
44D HIS* 3.4 0.5 - - - -
45D THR* 3.0 41.4 + - - +
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Residues in contact with SER 21 (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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63C GLN* 4.5 2.8 - - - +
64C ASP* 4.4 13.0 - - - +
67C HIS* 3.0 23.7 + - - -
133C ALA* 3.4 24.4 - - - +
18D ILE* 4.0 1.7 - - - +
20D GLU* 1.3 76.1 + - - +
22D ILE* 1.3 66.5 + - - +
23D LEU 4.3 0.5 + - - -
42D LEU* 4.8 6.2 - - - +
43D VAL 3.3 5.4 - - - -
44D HIS* 2.7 31.7 + - - -
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Residues in contact with ILE 22 (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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63C GLN* 3.8 11.9 - - + +
77C PHE* 5.5 4.0 - - + -
88C SER* 4.6 3.4 - - - +
187C HIS* 3.5 51.4 - - + +
189C SER* 4.5 5.4 - - - +
20D GLU* 4.1 24.2 - - + +
21D SER* 1.3 81.3 - - - +
23D LEU* 1.3 73.9 + - - +
24D MET* 3.8 12.5 + - + -
41D ILE 3.6 0.5 - - - +
42D LEU* 3.4 3.4 - - - -
43D VAL* 2.7 48.1 + - + +
45D THR* 6.1 0.2 - - - +
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Residues in contact with LEU 23 (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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63C GLN* 2.9 36.4 + - - +
134C HIS* 3.8 25.8 - - + +
167C HIS* 3.8 35.6 - - + +
22D ILE* 1.3 73.4 - - - +
24D MET* 1.3 66.5 + - - +
25D LEU* 5.1 2.0 - - + -
28D GLU* 4.5 1.6 - - - +
40D ASP* 4.0 31.2 - - + +
41D ILE 3.4 16.2 - - - +
42D LEU* 3.9 21.0 - - + +
61D ASP* 4.0 18.6 - - - +
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Residues in contact with MET 24 (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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187C HIS* 3.9 19.5 - - + -
189C SER* 3.9 19.7 - - - +
191C LEU* 4.2 15.0 - - + -
192C SER* 3.5 28.3 - - - +
22D ILE* 4.2 9.2 - - + +
23D LEU* 1.3 81.0 - - - +
25D LEU* 1.3 67.1 + - - +
28D GLU* 3.4 28.5 - - + +
29D VAL* 3.7 20.0 - - + -
40D ASP* 3.7 2.3 - - - +
41D ILE* 2.8 35.8 + - - +
43D VAL* 4.1 22.7 - - + -
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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