Contacts of the strand formed by residues 8 - 15 (chain B) in PDB entry 2QQ6
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 ARG 8 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.4 0.2 - - - +
7B THR* 1.3 84.0 + - - +
9B VAL* 1.3 67.9 + - - +
10B GLU* 6.0 0.9 - - + -
25B VAL* 3.4 4.3 - - - +
26B TRP* 2.8 53.2 + - + +
53B GLU* 3.8 5.6 - - - +
57B LEU* 4.0 0.6 - - - +
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.6 12.1 - - + -
8B ARG* 1.3 81.5 - - - +
10B GLU* 1.3 65.5 + - - +
23B VAL* 4.7 2.5 - - + -
24B ARG 3.6 6.3 - - - +
25B VAL* 4.3 18.8 - - + -
49B VAL* 4.5 20.9 - - + +
50B MSE 2.8 39.9 - - + +
53B GLU* 2.7 31.5 + - + +
56B LEU* 4.3 20.4 - - + -
57B LEU* 5.2 0.4 - - + -
92B ILE* 5.7 2.2 - - + -
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ARG* 6.0 1.1 - - + -
9B VAL* 1.3 74.8 - - - +
11B THR* 1.3 67.1 + - - +
23B VAL* 3.6 4.7 - - - +
24B ARG* 2.6 69.8 + - + +
26B TRP* 2.7 36.8 + - + +
50B MSE 4.4 3.4 - - - -
397B PHE* 2.7 40.0 - - + +
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Residues in contact with THR 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 1.3 77.4 - - - +
12B ALA* 1.3 61.6 + - - +
21B VAL* 4.0 11.9 - - + -
22B LEU 3.1 10.8 - - - +
23B VAL* 4.8 0.7 - - + -
46B HIS* 2.5 40.0 + - - +
49B VAL* 3.7 33.7 - - + -
50B MSE 3.7 13.8 - - - -
394B VAL* 3.7 4.2 - - - +
395B PRO 4.0 2.8 + - - +
396B PHE 3.8 2.8 - - - +
397B PHE* 2.8 31.5 + - - -
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 1.3 81.9 + - - +
13B ALA* 1.3 58.4 + - - +
14B ILE* 4.0 2.0 - - + -
20B SER 3.6 0.2 - - - +
21B VAL* 4.2 1.3 - - - -
22B LEU* 2.4 43.3 + - + +
394B VAL* 4.4 2.5 - - - -
395B PRO 4.3 9.4 - - - -
396B PHE* 4.4 14.6 - - + +
397B PHE* 3.4 37.5 - - + +
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA* 1.3 71.0 - - - +
14B ILE* 1.3 63.5 + - - +
20B SER 3.6 7.0 - - - +
21B VAL* 4.6 2.7 - - - -
42B ALA* 4.1 22.7 - - + -
388B ARG* 3.7 3.8 - - - +
389B HIS* 3.0 38.3 + - + +
391B LYS 5.5 0.2 - - - +
394B VAL* 3.9 31.3 + - + +
396B PHE* 5.2 6.0 - - - -
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Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA* 3.9 2.0 + - + +
13B ALA* 1.3 76.7 - - - +
15B ARG* 1.3 60.5 + - - +
16B ALA* 4.6 5.4 - - + +
19B PRO* 3.1 8.1 - - - +
20B SER* 2.8 42.5 + - - +
22B LEU* 4.1 33.4 - - + -
35B GLU* 4.3 6.5 - - - +
320B SER* 3.9 25.6 - - - +
353B PHE* 4.1 33.4 - - + -
384B ALA* 4.2 18.2 - - + +
387B HIS 3.9 6.1 - - - +
388B ARG* 4.6 2.0 - - - +
389B HIS* 4.2 3.2 - - - +
396B PHE* 5.2 6.5 - - + -
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Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 1.3 75.1 - - - +
16B ALA* 1.3 63.6 + - - +
18B GLY 4.4 4.0 - - - -
19B PRO* 4.6 3.6 - - + -
347B MSE 4.7 0.2 - - - +
349B HIS* 4.3 10.9 + - - -
353B PHE* 3.8 18.5 - - - -
387B HIS* 3.3 21.5 + - + +
388B ARG 4.6 5.4 - - - +
389B HIS* 5.2 8.5 - - + +
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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