Contacts of the strand formed by residues 101 - 107 (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 LYS 101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D SER 5.4 0.2 - - - -
44D GLN* 2.8 49.3 + - + +
48D LYS* 6.3 0.4 - - - +
100D ALA* 1.3 68.6 - - - +
102D TYR* 1.3 63.0 + - - +
103D PHE* 3.6 31.5 + - + -
124D GLN 3.6 21.4 + - - -
125D GLY* 4.2 2.5 - - - -
126D THR 3.5 13.0 - - - +
127D ILE* 3.8 38.1 - - + +
44E GLN* 6.0 2.0 - - - +
46E PRO* 6.0 5.3 - - - +
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Residues in contact with TYR 102 (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* 3.0 23.9 + - - -
21D LEU* 3.8 21.3 - - + -
41D TRP* 4.1 8.1 - - + -
42D TYR 3.4 7.4 - - - +
43D LYS* 3.5 27.7 - - + +
53D LEU* 3.6 32.5 - - + -
76D TYR* 4.4 3.9 + + - -
89D LEU* 3.9 11.4 - - + -
91D ILE* 3.7 18.3 - - + +
98D ASP* 2.9 44.4 + - - +
100D ALA 3.3 18.2 - - - -
101D LYS* 1.3 69.9 - - - +
103D PHE* 1.3 59.8 + - - +
125D GLY* 3.9 2.5 - - - -
126D THR* 3.0 20.4 + - - +
128D LEU* 3.7 17.7 - - + -
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Residues in contact with PHE 103 (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* 3.8 2.5 - - - -
41D TRP* 3.7 5.0 - - - -
42D TYR* 2.8 39.0 + - + +
44D GLN* 3.3 30.3 - - + -
50D MET* 3.9 27.6 - - + -
101D LYS* 3.8 39.9 - - + -
102D TYR* 1.3 73.2 - - - +
104D CYS* 1.3 59.7 + - - +
105D ALA 4.4 0.2 + - - -
122D PHE* 4.0 11.2 - + + -
123D GLY 4.3 11.7 - - - -
124D GLN* 3.6 22.0 - - - -
125D GLY* 3.5 11.0 - - - -
44E GLN* 4.7 7.9 - - + -
49E GLY* 5.4 4.7 - - - -
50E LEU* 3.9 25.1 - - + -
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Residues in contact with CYS 104 (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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4D VAL* 3.5 6.8 - - - +
6D GLN* 3.1 12.6 + - - +
23D CYS* 3.2 32.8 - - - -
39D ILE* 3.8 22.7 - - - -
40D PHE 3.5 4.3 - - - -
41D TRP* 3.7 38.8 - - + -
87D VAL* 4.4 0.7 - - - -
103D PHE* 1.3 75.1 - - - +
105D ALA* 1.3 65.5 + - - +
122D PHE* 3.5 1.5 - - - -
123D GLY 2.9 25.5 + - - -
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Residues in contact with ALA 105 (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* 4.7 1.3 - - - -
39D ILE* 3.6 8.2 - - - +
40D PHE* 2.8 39.4 + - + +
42D TYR* 4.7 0.4 - - + -
104D CYS* 1.3 77.9 - - - +
106D LEU* 1.3 59.9 + - - +
120D LEU* 3.8 26.2 - - + -
121D THR 3.3 7.0 - - - +
122D PHE* 3.7 29.6 - - + -
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Residues in contact with LEU 106 (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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3D LYS 4.8 4.7 - - - +
4D VAL* 3.6 24.7 - - + +
25D TYR* 4.5 7.4 - - + -
26D GLU 3.9 21.1 - - - +
27D THR* 4.0 11.7 - - + -
32D TYR* 4.0 26.0 - - + -
33D TYR 3.8 4.5 - - - +
39D ILE* 3.8 23.3 - - + -
105D ALA* 1.3 73.2 - - - +
107D GLY* 1.3 70.1 + - - +
108D GLU* 3.9 22.4 + - + +
119D LYS 4.5 0.5 - - - +
120D LEU* 3.5 9.8 - - - -
121D THR* 3.0 33.4 + - - +
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Residues in contact with GLY 107 (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* 3.4 9.0 - - - +
33D TYR 2.7 38.7 + - - -
40D PHE* 4.1 1.2 - - - -
106D LEU* 1.3 74.5 - - - +
108D GLU* 1.3 59.3 + - - -
119D LYS 5.0 1.6 - - - -
120D LEU* 3.8 11.2 - - - -
112E TYR* 3.6 26.9 - - - -
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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