Contacts of the strand formed by residues 33 - 38 (chain D) in PDB entry 5U07
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 33 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518C PRO* 6.3 1.8 - - + -
29D VAL* 4.4 0.2 - - - -
30D TYR 2.9 26.3 + - - +
31D GLY 3.1 8.4 - - - +
32D GLY* 1.3 80.4 - - - +
34D GLU* 1.3 74.4 + - - +
35D ARG* 3.4 15.5 + - - +
196D GLY* 4.5 11.0 - - - -
303D ALA* 3.5 32.3 - - + +
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Residues in contact with GLU 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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515C VAL 5.6 0.4 - - - +
518C PRO* 3.0 44.5 - - - +
519C TYR* 4.3 16.0 + - + +
27D THR* 5.1 13.5 - - + +
28D VAL 4.0 0.2 - - - -
29D VAL* 3.8 22.0 - - + +
32D GLY 4.1 3.7 + - - +
33D LYS* 1.3 80.6 - - - +
35D ARG* 1.3 60.2 + - - +
196D GLY* 3.5 5.9 - - - -
197D THR 3.5 36.3 + - - +
198D THR* 4.5 1.2 - - - +
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Residues in contact with ARG 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D THR* 4.4 3.3 - - - -
28D VAL* 2.9 41.0 + - + +
30D TYR* 2.9 38.0 + - + -
31D GLY* 4.5 0.8 - - - -
33D LYS* 3.4 7.1 + - - +
34D GLU* 1.3 74.6 - - - +
36D THR* 1.3 62.5 + - - +
37D ARG* 4.6 0.2 - - - +
192D PHE* 3.4 31.0 - - + -
193D THR* 2.9 36.7 + - - +
194D VAL 3.6 8.7 + - - -
195D HIS 3.7 7.6 + - - +
197D THR* 3.9 5.8 - - - -
300D PHE* 2.8 24.4 + - - +
301D GLU 4.2 3.0 + - - -
303D ALA* 3.3 35.2 - - - +
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Residues in contact with THR 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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25D PRO* 4.1 13.0 - - + +
26D LYS 3.5 12.1 - - - +
27D THR* 4.2 10.7 - - - +
35D ARG* 1.3 73.8 - - - +
37D ARG* 1.3 68.6 - - - +
38D VAL* 5.6 0.7 - - + -
192D PHE* 3.4 1.2 - - - -
193D THR* 3.0 34.0 + - - +
197D THR* 3.1 23.5 + - - +
199D VAL* 5.8 1.9 - - - +
227D SER* 3.4 27.4 + - - +
228D ALA 6.5 0.9 - - - -
231D PHE* 4.1 23.2 - - + -
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Residues in contact with ARG 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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18D ASN* 3.4 13.3 - - - +
26D LYS* 2.8 44.0 + - + +
27D THR* 4.2 4.2 + - - +
28D VAL* 2.9 37.5 - - + +
36D THR* 1.3 80.4 - - - +
38D VAL* 1.3 62.2 + - - +
39D SER* 3.5 20.0 + - - +
190D HIS* 3.5 30.2 + - + -
191D ALA 3.0 20.6 - - - +
192D PHE* 4.2 3.8 - - + +
231D PHE* 5.0 2.0 - - - -
12N MET* 3.7 11.7 - - - -
72N ASP* 3.4 37.2 + - - +
107N TYR* 3.6 17.1 + - - -
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Residues in contact with VAL 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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12D LEU* 5.8 0.7 - - + -
17D ILE* 4.1 28.0 - - + +
18D ASN* 3.4 15.9 - - - +
36D THR* 5.6 0.9 - - + -
37D ARG* 1.3 76.7 - - - +
39D SER* 1.3 71.3 + - - +
40D SER* 4.4 0.2 - - - -
42D SER* 4.6 4.9 - - - +
43D TRP* 5.1 13.6 - - + +
190D HIS* 4.3 0.2 - - - -
191D ALA* 3.2 39.5 + - + +
231D PHE* 3.6 30.7 - - + -
233D ARG* 5.6 2.5 - - - -
268D PRO* 5.4 4.9 - - + -
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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
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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