Contacts of the strand formed by residues 39 - 45 (chain D) in PDB entry 1QD6
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 TYR 39 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C HDS 3.7 9.4 - - - +
37D THR* 3.8 26.5 - - - -
38D ASN* 1.3 75.7 - - - +
40D LEU* 1.3 61.6 + - - +
41D ILE* 4.0 23.8 - - + -
68D LYS* 3.5 28.6 + - + -
69D PHE* 3.2 5.7 - - - +
70D GLN* 3.0 67.4 + - + +
95D LYS* 5.5 2.1 - - - +
224D GLU* 4.3 8.0 + - - -
238D TYR* 3.7 28.5 - + + -
240D GLN* 3.1 26.4 + - - -
263D VAL 3.3 14.6 - - - +
264D MET* 4.0 4.9 - - + -
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C HDS 4.0 44.8 - - + +
39D TYR* 1.3 73.8 - - - +
41D ILE* 1.3 61.9 + - - +
67D VAL* 3.3 33.7 - - + -
68D LYS 3.6 2.2 - - - -
69D PHE* 3.6 17.0 - - + -
98D TRP* 6.0 0.2 - - + -
262D GLY* 3.4 1.7 - - - -
263D VAL* 2.8 45.4 + - + +
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Residues in contact with ILE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TYR* 4.0 11.2 - - + -
40D LEU* 1.3 80.1 - - - +
42D TYR* 1.3 60.1 + - - +
43D THR* 3.6 23.1 - - + -
67D VAL* 3.5 7.9 - - - +
68D LYS* 2.8 43.7 + - + +
238D TYR* 3.6 28.5 - - + +
240D GLN* 3.7 41.1 - - + +
260D GLY* 4.2 5.4 - - - +
261D VAL* 3.4 12.8 - - - +
262D GLY* 3.6 16.4 - - - +
263D VAL 4.4 0.4 - - - +
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Residues in contact with TYR 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ILE* 1.3 73.2 - - - +
43D THR* 1.3 63.4 + - - +
65D ASP* 2.5 42.4 + - + -
66D GLU* 3.9 6.5 - - - -
67D VAL* 3.6 29.2 - - + -
100D LEU* 4.4 13.9 - - + +
101D SER* 3.9 12.6 + - - -
260D GLY* 3.1 1.6 - - - -
261D VAL* 2.8 36.7 + - - +
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Residues in contact with THR 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ILE* 3.6 33.2 - - + +
42D TYR* 1.3 84.0 - - - +
44D GLN* 1.3 61.0 + - - +
65D ASP* 3.2 8.7 - - - +
66D GLU* 2.8 42.2 + - - +
68D LYS* 3.8 16.2 - - + +
240D GLN* 5.6 0.7 - - - +
258D ARG* 2.8 35.8 + - + +
259D VAL 3.1 10.5 - - - -
260D GLY* 3.8 4.3 - - - -
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Residues in contact with GLN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D THR* 1.3 74.1 - - - +
45D THR* 1.3 77.4 + - - +
46D SER* 5.1 1.4 - - - -
64D LYS* 3.4 30.4 - - + +
65D ASP* 4.1 9.0 - - + +
257D THR 4.0 0.5 - - - +
258D ARG* 3.4 4.9 - - - -
259D VAL* 2.9 41.3 + - + +
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Residues in contact with THR 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D GLN* 1.3 90.6 - - - +
46D SER* 1.3 64.4 + - - +
47D ASP 3.2 25.2 + - - +
48D LEU* 4.0 8.7 - - + +
64D LYS* 3.0 35.9 + - - +
256D GLN* 2.8 27.9 + - - +
257D THR 3.4 6.5 + - - -
258D ARG* 3.7 27.5 - - - +
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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