Contacts of the strand formed by residues 26 - 33 (chain I) 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 VAL 26 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22I GLN* 3.9 0.2 - - - +
24I GLU 3.8 8.3 - - - +
25I LYS* 1.3 79.2 - - - +
27I GLN* 1.3 74.7 + - - +
46I THR* 3.3 6.6 - - - +
47I LEU* 2.7 39.6 + - + +
49I SER 3.7 8.1 - - - +
50I GLU* 3.6 26.2 - - + +
51I PRO* 4.5 13.9 - - + -
93I PRO* 3.3 42.2 - - + +
94I ASN* 3.7 7.9 - - - +
95I LYS* 4.8 1.6 - - + -
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Residues in contact with GLN 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I GLN* 4.2 2.5 + - - +
26I VAL* 1.3 80.0 - - - +
28I ALA* 1.3 61.2 + - - +
29I MET 4.2 0.2 - - - -
44I THR* 3.8 10.8 - - + -
45I ARG 3.4 3.4 - - - -
46I THR* 5.4 0.7 - - + +
90I ARG* 3.6 34.5 + - - +
94I ASN* 2.8 31.6 + - + +
95I LYS 2.9 26.3 + - - +
177J GLU* 4.8 1.8 + - - -
180J TYR* 3.2 56.5 - - + +
181J ARG* 3.9 16.6 + - - +
184J LEU* 4.3 12.3 - - + +
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Residues in contact with ALA 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I VAL 4.2 0.4 + - - -
27I GLN* 1.3 74.0 - - - +
29I MET* 1.3 60.5 + - - +
30I TYR* 3.6 26.4 - - + -
44I THR* 3.3 4.3 - - - -
45I ARG* 2.9 35.9 + - + +
47I LEU* 3.9 24.2 - - + -
57I LEU* 4.2 7.4 - - + -
95I LYS* 3.4 9.0 - - + +
97I VAL* 4.3 6.3 - - + -
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Residues in contact with MET 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I GLN 4.2 0.6 - - - -
28I ALA* 1.3 71.0 - - - +
30I TYR* 1.3 58.9 + - - +
31I ILE* 3.9 5.4 - - + +
42I CYS* 3.6 28.0 - - + -
43I LYS 3.3 7.9 - - - +
44I THR* 3.4 22.0 - - - +
87I ASP* 5.3 0.7 - - - +
89I PHE* 5.9 2.2 - - - -
90I ARG* 3.5 26.8 - - - +
95I LYS 3.0 12.0 + - - +
96I LEU* 3.7 14.3 - - + -
97I VAL* 2.8 27.0 + - - +
223I PHE* 3.7 30.3 - - - -
227I ARG* 5.3 7.6 - - - +
173J ARG* 4.3 11.9 - - - +
177J GLU* 4.5 3.4 - - - +
710J CL 3.8 11.7 - - + -
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Residues in contact with TYR 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I ALA* 3.6 27.6 - - + -
29I MET* 1.3 76.1 - - - +
31I ILE* 1.3 61.5 + - - +
32I TRP* 3.3 4.7 - - + -
42I CYS* 2.9 25.6 - - - +
43I LYS 2.7 14.7 + - - +
45I ARG* 3.7 20.4 - - - -
57I LEU* 4.0 7.3 - - + +
58I PRO* 2.7 50.2 + - - +
60I TRP* 3.7 33.9 - + + -
79I LEU* 4.2 15.9 - - + -
81I PRO* 4.2 14.1 - - + -
97I VAL* 3.4 12.8 - - + -
99I CYS* 3.5 20.6 - - - -
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Residues in contact with ILE 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I MET* 3.9 7.6 - - + +
30I TYR* 1.3 79.4 - - - +
32I TRP* 1.3 66.5 + - - +
40I LEU* 4.0 22.0 - - + -
41I ARG 3.2 9.2 - - - +
42I CYS* 3.9 12.3 - - + -
96I LEU* 3.8 30.3 - - + -
97I VAL 2.7 21.5 + - - +
98I LEU* 3.8 14.9 - - + +
99I CYS* 2.9 28.8 + - - +
219I TRP 5.9 0.2 - - - +
220I VAL* 5.5 7.4 - - + -
223I PHE* 3.9 40.4 - - + -
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Residues in contact with TRP 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I TYR 3.3 23.3 - - - -
31I ILE* 1.3 78.0 - - - +
33I ILE* 1.3 81.6 + - - +
40I LEU* 3.3 8.5 - - - +
41I ARG* 2.8 65.4 + - + +
42I CYS* 3.6 9.0 - - - -
43I LYS* 3.9 14.4 - - + -
62I PHE* 3.3 58.3 - + + -
67I THR* 4.3 0.6 - - - +
69I GLN* 4.2 3.8 - - - +
79I LEU* 3.7 33.2 - - + -
98I LEU* 5.1 1.6 - - - -
99I CYS 4.3 7.9 - - - +
101I VAL* 3.6 17.3 - - + -
162J TYR* 4.6 2.0 - + - -
163J CYS* 3.9 26.2 - - + -
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Residues in contact with ILE 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I TRP* 1.3 85.9 - - - +
34I ASP* 1.3 62.4 + - - +
37I GLY* 3.7 36.6 - - - +
39I GLY 3.4 7.4 - - - +
40I LEU* 4.0 14.8 - - + -
69I GLN* 3.3 12.6 - - - +
98I LEU* 5.5 5.6 - - + -
99I CYS 5.1 2.3 + - - +
101I VAL* 3.9 8.2 - - + +
111I THR* 3.9 19.0 + - - +
112I ASN* 6.2 0.4 - - - -
113I LEU 6.1 0.9 - - - +
219I TRP* 3.4 43.7 - - + +
347I ASP* 4.0 8.7 - - - +
349I PHE* 4.6 9.0 - - + -
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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