Contacts of the strand formed by residues 50 - 57 (chain D) in PDB entry 4QRR
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 MET 50 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D TYR* 3.8 19.3 - - + -
43D LYS 3.6 0.9 - - - +
44D GLN* 3.6 36.1 - - - +
48D LYS 3.4 5.7 + - - +
49D GLU* 1.3 74.2 - - - +
51D ILE* 1.3 63.6 + - - +
52D PHE 4.3 0.4 - - - -
103D PHE* 3.9 12.8 - - + -
122D PHE* 3.7 30.5 - - + -
44E GLN* 5.0 0.2 - - - +
50E LEU* 3.8 26.2 - - + -
103E LEU* 4.8 4.5 - - + -
118E PHE* 3.6 54.4 + - + +
119E GLY 5.0 4.6 + - - -
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Residues in contact with ILE 51 (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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42D TYR* 3.2 7.2 - - - -
43D LYS* 2.8 57.4 + - + +
45D LEU* 3.7 34.3 - - + -
49D GLU* 4.0 17.0 - - + +
50D MET* 1.3 78.8 - - - +
52D PHE* 1.3 72.5 + - - +
53D LEU* 3.7 9.7 + - + +
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Residues in contact with PHE 52 (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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40D PHE* 3.6 14.6 - + + -
41D TRP 4.0 3.6 - - - -
42D TYR* 3.6 36.0 - + + -
50D MET 4.3 0.4 + - - -
51D ILE* 1.3 84.3 - - - +
53D LEU* 1.3 66.5 + - - +
54D ILE* 3.5 37.2 - - - -
55D ARG* 3.6 12.6 - - + -
115E GLU* 3.6 43.1 - - + -
116E GLN 4.4 5.8 - - - +
117E PHE* 5.1 17.0 - + + -
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Residues in contact with LEU 53 (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 TRP* 2.9 21.4 + - + +
42D TYR 3.7 13.9 - - - +
43D LYS* 3.7 18.6 - - + -
51D ILE* 3.9 11.9 - - + +
52D PHE* 1.3 86.1 - - - +
54D ILE* 1.4 65.4 + - + +
72D SER* 4.8 9.7 + - - -
76D TYR* 3.5 45.8 - - + +
89D LEU* 4.2 12.1 - - + -
102D TYR* 3.6 33.7 - - + -
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Residues in contact with ILE 54 (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 ILE 4.1 0.2 - - - +
40D PHE* 3.6 1.0 - - - -
41D TRP* 3.0 40.4 + - + -
52D PHE* 3.5 13.0 - - - -
53D LEU* 1.4 82.3 - - + +
55D ARG* 1.3 61.2 + - - +
56D GLN 5.6 0.2 - - - +
70D ALA* 3.7 36.8 - - + +
71D LYS* 3.7 1.1 - - - +
72D SER* 3.7 37.2 - - - +
76D TYR* 4.1 11.9 - - + +
77D SER 5.0 0.2 - - - +
78D VAL* 3.7 28.3 - - + -
89D LEU* 4.1 10.1 - - + -
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Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ALA 5.0 2.1 + - - -
150A ALA* 3.0 39.0 + - - +
151A ARG* 3.9 12.6 + - - +
33D TYR* 3.3 27.1 - - + -
39D ILE 3.3 11.4 - - - +
40D PHE* 3.5 17.9 - - + -
52D PHE* 3.6 17.7 - - + -
54D ILE* 1.3 77.7 - - - +
56D GLN* 1.3 62.9 + - - +
57D GLY 4.2 0.4 - - - -
67D GLU* 3.0 35.3 + - - +
70D ALA* 3.6 16.1 - - - +
113E TYR* 2.8 39.8 + - - +
115E GLU* 4.9 13.1 + - - +
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Residues in contact with GLN 56 (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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33D TYR* 3.5 3.7 - - - -
39D ILE* 2.7 54.5 + - + +
41D TRP* 5.9 0.9 - - + -
54D ILE* 4.3 0.4 - - - +
55D ARG* 1.3 73.1 - - - +
57D GLY* 1.3 87.4 + - - +
67D GLU* 3.2 19.6 + - - +
68D GLN 3.5 8.7 + - - -
69D ASN* 3.3 5.5 - - - -
70D ALA* 2.7 30.8 + - - +
78D VAL* 3.3 25.0 - - + +
80D PHE* 3.8 35.5 - - + +
87D VAL* 4.8 2.9 - - + -
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Residues in contact with GLY 57 (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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32D TYR 3.8 0.2 - - - -
33D TYR* 3.6 20.4 - - - -
56D GLN* 1.3 93.5 + - - +
58D SER* 1.3 62.3 + - - -
66D ASP 3.1 3.4 - - - -
67D GLU* 2.9 40.9 + - - +
80D PHE* 4.6 2.1 - - - -
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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