Contacts of the strand formed by residues 30 - 36 (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 GLU 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A TRP* 3.0 9.5 - - - -
27A ALA 2.6 38.1 + - - +
28A GLY 3.2 1.0 - - - -
29A ASP* 1.3 82.7 - - + +
31A HIS* 1.3 76.7 + - - +
99A LEU* 3.8 14.8 - - + -
102A LYS* 3.9 35.7 + - - +
103A LEU* 4.2 19.4 + - + -
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Residues in contact with HIS 31 (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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24A ARG* 3.2 35.8 + - + -
25A VAL 3.0 11.7 - - - +
26A TRP* 3.3 40.0 - + + +
29A ASP 4.8 0.6 + - - -
30A GLU* 1.3 83.0 + - - +
32A GLY* 1.3 57.6 + - - +
33A LEU* 4.8 6.0 - - + +
99A LEU* 3.5 8.5 - - - +
102A LYS* 2.6 57.1 + - - -
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Residues in contact with GLY 32 (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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24A ARG* 3.4 9.4 - - - +
25A VAL 3.0 28.9 + - - -
31A HIS* 1.3 77.9 - - - +
33A LEU* 1.3 61.2 + - - -
95A ALA* 3.5 23.6 - - - +
98A ASP* 3.3 11.7 - - - -
99A LEU* 3.7 5.9 - - - +
102A LYS* 4.4 0.4 - - - -
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Residues in contact with LEU 33 (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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22A LEU* 4.1 17.0 - - + -
23A VAL 3.5 14.6 - - - +
24A ARG* 4.4 13.7 - - + +
31A HIS* 5.1 5.8 - - + +
32A GLY* 1.3 75.4 - - - -
34A GLY* 1.3 73.0 - - - +
94A THR* 3.9 1.6 - - - +
95A ALA* 3.6 11.3 + - - -
98A ASP* 2.5 21.2 + - - +
322A VAL* 4.2 29.7 - - + +
354A VAL* 5.4 0.7 - - + -
375A LEU* 3.7 17.9 - - + +
377A LEU* 6.1 4.0 - - + -
379A LEU* 3.6 41.3 - - + +
397A PHE* 5.7 1.3 - - + -
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Residues in contact with GLY 34 (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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22A LEU* 3.2 6.6 - - - +
23A VAL 2.7 40.5 + - - -
33A LEU* 1.3 80.6 - - - +
35A GLU* 1.3 59.3 + - - +
91A GLY* 3.3 24.5 - - - -
94A THR* 4.0 5.8 - - - -
95A ALA* 3.9 3.1 - - - +
322A VAL* 4.5 4.3 - - - -
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Residues in contact with GLU 35 (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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14A ILE* 4.4 1.8 - - - +
16A ALA* 5.0 0.2 - - - +
20A SER* 3.5 24.7 + - - -
21A VAL 3.5 3.1 - - - +
22A LEU* 4.2 11.9 - - + +
34A GLY* 1.3 74.2 - - - +
36A CYS* 1.3 63.9 + - - +
91A GLY* 3.3 17.2 + - - -
94A THR* 4.6 6.6 + - - +
291A ALA* 3.8 14.5 - - + +
319A SER* 2.8 20.9 - - - -
320A SER* 2.6 49.4 + - - -
322A VAL* 3.1 8.4 - - + +
323A GLY* 2.8 35.5 + - - +
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Residues in contact with CYS 36 (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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20A SER* 3.5 17.7 - - - -
21A VAL* 2.8 18.2 + - + +
23A VAL* 3.9 17.7 - - - -
35A GLU* 1.3 76.4 - - - +
37A TYR* 1.3 69.1 + - - +
38A PRO 3.2 2.3 - - - -
45A ILE* 3.8 37.1 - - + +
49A VAL* 4.5 0.4 - - - -
87A THR* 3.6 20.9 - - + +
88A ALA 3.9 7.0 - - - -
91A GLY* 3.6 18.6 - - - -
291A ALA* 3.9 3.6 - - - -
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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