Contacts of the strand formed by residues 33 - 44 (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 TYR 33 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ALA 4.1 3.6 + - - -
151A ARG 3.9 11.6 + - - -
155A GLN* 3.6 44.0 + - + +
32D TYR* 1.3 80.8 - - - +
39D ILE* 1.3 62.5 + - - +
40D PHE* 3.6 22.0 - - + -
55D ARG* 3.3 40.2 - - + -
56D GLN 3.5 2.0 - - - -
57D GLY* 3.6 19.5 - - - -
67D GLU* 3.7 11.3 + - + +
106D LEU* 3.6 2.8 - - - +
107D GLY 2.7 36.3 + - - -
112E TYR* 3.6 20.0 - + - +
113E TYR* 3.7 25.8 - - + -
7P HIS* 4.6 4.2 + - - -
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Residues in contact with ILE 39 (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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4D VAL* 6.1 0.4 - - + -
25D TYR* 3.9 28.3 - - + -
32D TYR* 4.6 4.3 - - + -
33D TYR* 1.3 72.8 - - - +
40D PHE* 1.3 62.2 + - - +
41D TRP* 4.0 9.6 - - + +
54D ILE 4.7 0.2 - - - -
55D ARG* 3.3 8.1 - - - +
56D GLN* 2.7 47.3 + - + +
80D PHE* 4.4 17.7 - - + -
87D VAL* 3.8 27.1 - - + -
104D CYS* 3.8 24.9 - - - -
105D ALA 3.6 4.3 - - - +
106D LEU* 3.8 33.2 - - + -
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Residues in contact with PHE 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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33D TYR* 3.6 25.6 - - + -
39D ILE* 1.3 74.9 - - - +
41D TRP* 1.3 62.6 + - - +
42D TYR* 3.7 19.6 - - + -
52D PHE* 3.6 20.9 - + + -
54D ILE 3.6 3.6 - - - -
55D ARG* 3.5 20.2 - - + -
103D PHE 4.2 0.2 - - - +
104D CYS* 3.5 4.7 - - - -
105D ALA* 2.8 45.4 + - + +
107D GLY* 4.1 0.7 - - - -
120D LEU* 3.7 26.0 - - + -
112E TYR 3.2 27.1 - - - -
113E TYR 3.8 7.6 - - - -
114E ASN 3.3 29.8 - - - -
115E GLU* 3.6 8.3 - - - -
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Residues in contact with TRP 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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6D GLN* 4.2 6.7 - - - -
21D LEU* 3.3 37.2 - - + -
22D ASN 4.6 0.2 - - - -
23D CYS* 3.8 14.8 - - + -
39D ILE* 4.0 19.2 - - + +
40D PHE* 1.3 75.2 - - - +
42D TYR* 1.3 65.7 + - - +
52D PHE* 3.9 1.7 - - - -
53D LEU* 2.9 35.8 + - + +
54D ILE* 3.0 25.7 + - + +
56D GLN* 5.9 1.3 - - + -
78D VAL* 3.6 27.1 - - + +
87D VAL* 3.7 20.7 - - - +
89D LEU* 3.6 32.3 - - + +
102D TYR* 4.1 20.9 - - + -
103D PHE 3.7 14.6 - - - -
104D CYS* 3.7 21.8 - - + -
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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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40D PHE* 3.7 28.2 - - + +
41D TRP* 1.3 77.4 - - - +
43D LYS* 1.3 59.2 + - - +
44D GLN 4.3 0.2 - - - -
50D MET* 3.8 31.2 - - + -
51D ILE* 3.2 17.7 - - - -
52D PHE* 3.6 26.5 - + + -
53D LEU* 3.7 3.1 - - - -
102D TYR* 3.4 12.0 - - - +
103D PHE* 2.8 34.8 + - + +
105D ALA* 4.7 0.2 - - + -
120D LEU* 4.0 7.1 - - + +
122D PHE* 3.7 25.4 - + - -
115E GLU* 4.3 0.7 - - - -
116E GLN* 2.7 49.5 + - - +
118E PHE* 3.7 17.3 - + - -
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Residues in contact with LYS 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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42D TYR* 1.3 73.6 - - - +
44D GLN* 1.3 59.7 + - - +
45D LEU* 3.9 20.0 + - - +
49D GLU 3.3 4.0 - - - +
50D MET* 4.6 1.8 - - - -
51D ILE* 2.8 51.9 + - + +
53D LEU* 3.7 28.5 - - + -
76D TYR* 4.4 6.0 + - - +
97D GLU* 2.8 34.2 + - - +
98D ASP* 3.8 8.8 + - - +
100D ALA* 3.7 15.0 - - + -
101D LYS 3.8 2.7 - - - -
102D TYR* 3.5 31.7 + - + +
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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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42D TYR 4.3 0.2 - - - -
43D LYS* 1.3 72.2 - - - +
45D LEU* 1.3 64.4 + - - +
48D LYS* 3.4 48.4 + - - +
49D GLU 3.4 3.4 - - - +
50D MET* 3.6 25.6 - - - +
100D ALA* 3.3 3.5 - - - +
101D LYS* 2.8 49.2 + - + +
103D PHE* 3.3 19.3 - - + -
44E GLN* 2.7 39.4 + - - +
101E LEU* 4.5 0.2 - - - +
103E LEU* 4.3 6.9 - - - +
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Residues in contact with LEU 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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43D LYS* 3.9 26.0 - - - +
44D GLN* 1.3 77.8 - - - +
46D PRO* 1.4 71.2 - - + +
47D SER* 3.0 16.8 - - - +
48D LYS* 2.8 24.1 + - - -
49D GLU* 3.3 32.6 + - + +
51D ILE* 3.7 21.1 - - + -
97D GLU 4.2 8.5 - - - +
99D SER 4.3 2.9 - - - +
100D ALA* 3.9 7.2 - - + -
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Residues in contact with PRO 46 (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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45D LEU* 1.4 92.1 - - + +
47D SER* 1.4 54.9 + - - +
48D LYS* 3.1 26.9 + - - +
99D SER 4.3 13.2 - - - +
100D ALA* 5.1 2.2 - - + -
187E PRO* 4.2 38.3 - - + +
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Residues in contact with SER 47 (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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45D LEU* 3.0 9.8 + - - +
46D PRO* 1.4 76.6 - - - +
48D LYS* 1.4 65.0 + - - +
49D GLU* 3.1 26.9 + - - +
120E PRO 4.8 4.7 - - - +
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Residues in contact with LYS 48 (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* 3.4 31.4 + - - +
45D LEU 2.8 14.3 + - - -
46D PRO* 3.1 22.4 + - - +
47D SER* 1.4 77.4 - - - +
49D GLU* 1.4 61.4 + - - +
50D MET 3.4 2.1 + - - -
101D LYS* 6.3 1.0 - - - +
44E GLN* 5.0 6.1 - - - +
101E LEU* 3.8 24.6 - - + +
103E LEU* 4.5 8.3 - - - +
120E PRO 4.2 11.3 - - - +
123E ARG* 3.7 29.2 - - - +
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Residues in contact with GLU 49 (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 LYS 3.3 5.9 - - - +
44D GLN* 3.4 1.1 - - - -
45D LEU* 3.3 46.3 + - + +
47D SER* 3.1 19.3 + - - +
48D LYS* 1.4 74.3 - - - +
50D MET* 1.3 62.9 + - - +
51D ILE* 3.8 17.6 + - + +
118E PHE 6.1 0.9 - - - +
119E GLY 5.4 2.5 - - - +
120E PRO* 5.0 13.9 - - + -
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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