Contacts of the strand formed by residues 40 - 47 (chain D) in PDB entry 2QC8
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 LEU 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D ILE* 3.9 17.5 - - + -
32D TRP* 3.3 11.7 - - - +
33D ILE* 4.1 10.8 - - + -
38D GLU 3.8 2.2 + - - +
39D GLY* 1.3 77.2 - - - -
41D ARG* 1.3 68.1 + - - +
98D LEU* 5.1 2.0 - - + -
219D TRP* 3.6 46.7 - - + +
222D ARG* 4.1 3.8 - - + -
223D PHE* 3.8 43.1 - - + +
226D HIS* 4.1 17.4 - - + +
238D PHE* 5.9 0.2 - - + -
163E CYS 4.3 1.0 - - - +
164E GLY* 4.6 0.3 - - - -
165E VAL* 3.7 24.4 + - + +
169E ARG* 6.1 0.2 - - - -
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Residues in contact with ARG 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ILE* 3.2 7.2 - - - +
32D TRP* 2.7 59.4 + - + +
34D ASP* 3.1 41.0 + - + +
36D THR* 5.7 2.6 - - - +
40D LEU* 1.3 79.7 + - - +
42D CYS* 1.3 63.2 + - - +
66D SER 3.5 10.1 + - - -
67D THR* 3.9 26.5 + - + +
223D PHE* 5.1 1.3 - - - -
159E GLY 3.1 29.1 + - - -
160E PRO* 3.7 19.3 - - - +
162E TYR* 2.8 36.6 + - - +
163E CYS* 3.1 11.7 - - + +
164E GLY* 4.5 2.5 - - - -
165E VAL* 5.5 0.7 - - - -
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Residues in contact with CYS 42 (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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29D MET* 3.7 35.4 - - + -
30D TYR 3.0 13.7 - - - +
31D ILE* 4.2 1.3 - - + -
32D TRP* 3.7 3.1 - - - -
41D ARG* 1.3 78.9 - - - +
43D LYS* 1.3 63.9 + - - +
223D PHE* 3.7 23.6 - - + -
163E CYS* 2.7 39.3 + - - +
164E GLY 4.8 2.7 - - - -
165E VAL* 4.9 0.9 - - - -
173E ARG* 4.4 18.2 - - - -
194E ASN* 5.0 1.4 - - - +
195E ALA 5.3 0.3 + - - -
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Residues in contact with LYS 43 (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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28D ALA 3.9 0.2 - - - +
29D MET* 3.4 2.1 - - - -
30D TYR* 2.7 34.9 + - - +
32D TRP* 4.0 13.0 - - + -
42D CYS* 1.3 78.3 - - - +
44D THR* 1.3 59.3 + - - +
60D TRP* 3.4 43.6 - - + +
61D ASN* 2.8 31.0 + - - +
62D PHE* 4.2 16.3 - - - +
79D LEU* 4.6 1.6 - - - -
704D CL 3.8 10.1 - - - -
162E TYR* 5.0 4.0 + - - +
163E CYS* 4.0 7.9 - - - -
193E THR 3.6 9.4 - - - +
194E ASN* 3.7 21.8 - - + +
205E GLN* 6.2 0.4 - - - +
501E ADP 4.8 15.2 + - - -
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Residues in contact with THR 44 (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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27D GLN* 3.9 3.8 - - + -
28D ALA 3.3 15.3 - - - +
29D MET* 3.6 5.7 - - - +
43D LYS* 1.3 76.5 - - - +
45D ARG* 1.3 70.2 + - - +
60D TRP* 3.6 9.8 - - - -
90D ARG* 3.0 35.1 + - - +
704D CL 3.0 21.7 - - - +
180E TYR* 3.6 18.6 - - + +
192E GLY* 3.1 2.8 - - - -
193E THR* 3.0 36.7 + - - +
205E GLN* 4.4 0.2 - - - +
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Residues in contact with ARG 45 (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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27D GLN* 3.6 3.1 - - - -
28D ALA* 3.0 34.1 + - + +
30D TYR* 3.6 32.2 + - + -
44D THR* 1.3 75.3 - - - +
46D THR* 1.3 62.1 + - - +
47D LEU* 4.0 20.2 + - + +
58D PRO* 3.8 19.8 - - - +
59D GLU 3.1 26.5 + - - -
60D TRP* 3.2 48.0 - - + +
180E TYR* 3.5 4.5 - - - -
191E ALA 3.4 8.5 - - - +
192E GLY* 4.1 0.2 - - - -
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Residues in contact with THR 46 (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 LYS* 3.6 37.5 - - + -
26D VAL 3.4 7.4 - - - +
45D ARG* 1.3 78.6 + - - +
47D LEU* 1.3 70.2 + - - +
48D ASP* 5.5 0.7 - - - +
180E TYR* 2.7 22.1 + - + +
184E LEU* 4.4 7.6 - - + -
190E ILE 2.6 27.7 + - - +
191E ALA* 2.7 18.9 + - - +
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Residues in contact with LEU 47 (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 LYS* 3.5 6.6 - - - +
26D VAL* 2.7 39.5 + - + +
28D ALA* 3.9 18.2 - - + -
45D ARG* 4.1 15.9 - - + +
46D THR* 1.3 81.5 - - - +
48D ASP* 1.3 65.6 + - - +
49D SER 3.3 10.3 + - - +
51D PRO* 4.1 20.2 - - + -
57D LEU* 3.8 27.1 - - + -
58D PRO* 4.0 29.6 - - + -
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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