Contacts of the strand formed by residues 40 - 47 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ILE* 3.8 21.8 - - + -
32A TRP 3.3 8.1 - - - +
33A ILE* 4.1 10.5 - - + -
38A GLU 3.6 2.2 + - - +
39A GLY* 1.3 77.1 - - - -
41A ARG* 1.3 68.4 + - - +
98A LEU* 4.9 4.0 - - + -
219A TRP* 3.7 39.3 - - + +
222A ARG* 4.2 6.5 - - + -
223A PHE* 3.7 48.0 - - + +
226A HIS* 4.2 13.9 - - + +
164B GLY* 4.5 0.3 - - - -
165B VAL* 3.7 25.1 + - + +
169B ARG* 6.0 0.3 - - - -
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 3.3 4.9 - - - +
32A TRP* 2.8 60.6 + - + +
34A ASP* 3.0 43.9 + - + +
36A THR* 5.6 2.8 - - - +
40A LEU* 1.3 81.6 + - - +
42A CYS* 1.3 66.9 + - - +
66A SER 3.8 8.3 + - - -
67A THR* 4.1 23.5 + - + +
68A LEU* 5.9 0.8 - - - +
223A PHE* 5.0 1.6 - - - -
159B GLY 3.0 29.5 + - - -
160B PRO* 3.5 19.8 + - - +
162B TYR 2.8 36.1 + - - -
163B CYS* 3.0 10.8 - - + +
164B GLY* 4.5 2.5 - - - -
165B VAL* 5.5 0.2 - - - -
169B ARG* 6.1 0.8 - - - +
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Residues in contact with CYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A MET* 3.6 33.2 - - + -
30A TYR 3.0 14.6 - - - +
31A ILE* 4.2 1.1 - - - -
32A TRP* 3.6 6.3 - - - -
41A ARG* 1.3 78.4 - - - +
43A LYS* 1.3 62.3 + - - +
223A PHE* 3.7 26.5 - - + -
163B CYS* 2.7 35.9 + - - +
164B GLY 4.7 7.0 - - - -
165B VAL* 5.0 1.3 - - - -
173B ARG* 4.6 12.6 - - - -
194B ASN* 5.0 2.1 - - - +
195B ALA 5.2 0.5 + - - -
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA 3.7 0.3 - - - +
29A MET* 4.3 1.6 - - - -
30A TYR* 2.8 35.2 + - + +
32A TRP* 4.0 11.7 - - + -
42A CYS* 1.3 78.0 - - - +
44A THR* 1.3 60.6 + - - +
60A TRP* 3.5 41.1 - - + +
61A ASN* 2.7 33.1 + - - +
62A PHE* 4.1 14.8 - - - +
79A LEU* 4.6 2.7 - - - -
162B TYR* 4.9 3.9 + - - +
163B CYS* 3.9 8.3 - - - -
193B THR 3.6 9.4 - - - +
194B ASN* 3.7 21.1 - - + +
205B GLN* 6.3 0.4 - - - +
501B ADP 4.9 13.9 + - - -
705B CL 3.9 8.5 - - - -
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLN* 3.8 8.1 - - + -
28A ALA 3.2 9.9 - - - +
29A MET* 3.4 8.5 - - - +
43A LYS* 1.3 76.2 - - - +
45A ARG* 1.3 68.0 + - - +
60A TRP* 3.6 9.5 - - - -
90A ARG* 3.1 40.2 + - - +
180B TYR* 3.6 22.2 - - + +
192B GLY* 3.1 3.2 - - - -
193B THR* 3.1 35.6 + - - +
205B GLN* 4.6 0.2 - - - +
705B CL 3.1 13.4 - - - +
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Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLN* 3.6 2.3 - - - -
28A ALA* 2.9 42.6 + - + +
30A TYR* 3.8 18.2 + - + -
44A THR* 1.3 74.3 - - - +
46A THR* 1.3 61.6 + - - +
47A LEU* 3.8 17.4 + - + +
58A PRO* 3.7 24.6 - - - +
59A GLU 3.6 10.9 + - - -
60A TRP* 3.3 65.4 - - + +
180B TYR* 3.4 5.4 - - - -
191B ALA 3.4 9.4 - - - +
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 3.6 35.7 - - + -
26A VAL 3.2 8.5 - - - +
27A GLN* 4.8 0.2 - - - +
45A ARG* 1.3 76.0 + - - +
47A LEU* 1.3 69.6 + - - +
48A ASP* 5.5 0.8 - - - +
180B TYR* 2.4 26.5 + - + -
184B LEU* 4.3 7.6 - - + -
190B ILE 2.7 28.4 + - - +
191B ALA* 2.8 16.7 + - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 3.4 6.9 - - - +
26A VAL* 2.6 42.8 + - + +
28A ALA* 3.7 18.4 - - + -
45A ARG* 4.2 15.5 - - + +
46A THR* 1.3 81.2 - - - +
48A ASP* 1.3 64.5 + - - +
49A SER 3.3 11.4 - - - +
51A PRO* 3.9 22.2 - - + -
57A LEU* 3.6 28.5 - - + -
58A PRO* 3.9 28.9 - - + -
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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