Contacts of the strand formed by residues 20 - 27 (chain A) 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 SER 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ALA* 3.4 4.2 - - - +
14A ILE* 2.9 40.6 + - - +
16A ALA* 3.9 14.2 + - - +
19A PRO* 1.3 75.2 - - - +
21A VAL* 1.3 62.9 + - - +
35A GLU* 3.5 29.0 + - - -
36A CYS 3.5 15.3 - - - -
38A PRO* 3.7 20.1 - - - +
318A VAL 4.8 0.3 + - - -
319A SER* 4.5 3.7 - - - -
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Residues in contact with VAL 21 (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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11A THR* 4.2 19.3 - - + -
12A ALA 3.3 11.0 - - - +
13A ALA* 4.4 5.6 - - + -
19A PRO 4.9 0.7 - - - +
20A SER* 1.3 79.0 - - - +
22A LEU* 1.3 74.4 + - - +
23A VAL* 4.6 4.7 - - + -
35A GLU* 3.5 0.9 - - - -
36A CYS* 2.8 42.7 + - + +
42A ALA* 3.8 38.8 - - + +
45A ILE* 4.3 20.0 - - + -
46A HIS* 5.0 5.6 - - - -
49A VAL* 5.6 0.2 - - + -
394A VAL* 5.1 3.6 - - + -
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Residues in contact with LEU 22 (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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11A THR* 3.2 6.5 - - - -
12A ALA* 2.6 48.3 + - + +
14A ILE* 3.2 53.6 - - + +
20A SER 4.4 0.7 - - - -
21A VAL* 1.3 79.5 - - - +
23A VAL* 1.3 61.0 + - - +
33A LEU* 4.1 19.7 - - + -
34A GLY 3.2 11.7 - - - +
35A GLU* 4.2 17.3 - - + -
322A VAL* 4.5 16.2 - - + -
379A LEU* 5.3 11.0 - - + -
397A PHE* 4.9 5.8 - - + -
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Residues in contact with VAL 23 (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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9A VAL* 4.2 12.1 - - + -
10A GLU 3.6 6.3 - - - +
11A THR* 4.5 3.1 - - + -
21A VAL* 4.3 2.9 - - + +
22A LEU* 1.3 79.9 - - - +
24A ARG* 1.3 63.1 + - - +
25A VAL* 4.2 5.4 - - + -
33A LEU* 3.5 4.6 - - - +
34A GLY* 2.7 40.6 + - - +
36A CYS* 3.9 28.5 - - - -
49A VAL* 3.6 34.1 - - + -
91A GLY 4.2 14.8 - - - +
92A ILE* 4.1 14.8 - - + -
95A ALA* 3.8 3.5 - - - +
397A PHE* 5.7 0.2 - - - -
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Residues in contact with ARG 24 (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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8A ARG 3.8 0.7 - - - +
9A VAL* 3.3 5.4 - - - +
10A GLU* 2.7 54.5 + - + +
22A LEU 4.3 0.2 - - - -
23A VAL* 1.3 73.2 - - - +
25A VAL* 1.3 62.9 + - - +
26A TRP* 3.4 28.0 - - - +
31A HIS* 3.2 36.7 + - + -
32A GLY 3.4 8.1 - - - +
33A LEU* 4.4 11.5 - - + +
379A LEU* 5.4 7.4 - - - +
381A GLU* 3.8 28.6 + - - +
397A PHE* 2.9 53.6 - - + +
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Residues in contact with VAL 25 (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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6A ILE* 4.1 18.4 - - + -
8A ARG 3.6 2.9 - - - +
9A VAL* 4.0 22.9 - - + -
23A VAL* 4.6 8.7 - - + -
24A ARG* 1.3 75.9 - - - +
26A TRP* 1.3 64.7 + - - +
31A HIS* 3.0 4.0 - - - -
32A GLY 3.0 29.4 + - - +
56A LEU* 5.5 1.1 - - + -
92A ILE* 4.6 9.2 - - + +
95A ALA* 3.4 28.3 - - + -
96A LEU* 3.9 27.1 - - + -
99A LEU* 3.7 14.3 - - + +
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Residues in contact with TRP 26 (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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6A ILE* 3.5 4.5 - - - +
7A THR* 2.5 35.5 + - + -
8A ARG* 2.8 35.8 + - + +
10A GLU* 3.0 28.0 + - + -
24A ARG* 3.4 44.5 - - - +
25A VAL* 1.3 77.0 - - - +
27A ALA* 1.3 52.3 + - - +
28A GLY 3.5 12.3 - - - +
29A ASP* 2.9 29.2 - - - -
30A GLU 3.0 21.1 - - - +
31A HIS* 3.3 26.0 - + + -
99A LEU* 4.7 1.6 - - - -
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Residues in contact with ALA 27 (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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4A PRO* 4.5 8.0 - - + +
5A ARG 3.0 29.6 + - - +
7A THR* 3.5 1.1 - - - -
25A VAL 4.1 0.6 + - - -
26A TRP* 1.3 71.4 - - - +
28A GLY* 1.3 60.2 + - - +
29A ASP 3.5 3.2 + - - -
30A GLU* 2.6 17.3 + - + +
61A PRO* 4.2 3.4 - - + -
99A LEU* 3.9 28.3 - - + -
103A LEU* 4.1 14.2 - - + +
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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