Contacts of the strand formed by residues 106 - 111 (chain d) in PDB entry 4PJO
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 VAL 106 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44d ILE* 4.1 10.5 - - + -
45d ASN 4.2 2.2 - - - -
47d ARG* 4.7 0.6 - - - +
63d CYS* 4.0 24.5 - - + +
65d MET* 4.8 5.2 - - - -
101d LEU* 4.1 21.3 - - + -
103d GLY* 2.8 17.9 + - - +
104d ASP 3.7 7.8 - - - +
105d SER* 1.3 80.1 - - - +
107d ILE* 1.3 65.0 + - - +
108d VAL 3.6 13.2 - - - +
109d VAL* 3.7 23.1 - - + -
63f LEU* 6.1 0.4 - - + -
65f ARG* 3.7 19.2 - - + +
67f ASN* 4.2 0.2 - - - +
68f ASN* 3.1 16.1 + - - +
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Residues in contact with ILE 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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45d ASN* 3.0 33.1 + - + +
46d CYS 3.7 22.2 - - - +
47d ARG* 3.7 23.8 - - + +
106d VAL* 1.3 75.9 - - - +
108d VAL* 1.3 79.0 + - + +
23f LEU* 4.1 17.0 - - + -
25f TRP* 4.2 13.7 - - + +
27f MET* 4.9 3.4 - - + -
29f TYR* 5.4 0.2 - - - +
64f ILE* 3.9 1.9 - - - +
65f ARG 3.2 23.2 + - - -
68f ASN* 3.2 29.6 + - - +
38k TYR* 4.6 12.8 - - + -
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Residues in contact with VAL 108 (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 LEU 3.8 0.2 - - - +
44d ILE* 3.3 5.2 - - - +
45d ASN* 3.0 32.3 + - + -
106d VAL* 4.2 1.1 - - - -
107d ILE* 1.3 92.8 - - + +
109d VAL* 1.3 68.7 + - - +
23f LEU* 4.5 0.2 - - + -
29f TYR* 3.9 33.4 - - + +
62f VAL* 4.1 15.0 - - + -
63f LEU 3.4 10.5 - - - +
64f ILE* 4.0 17.0 - - + -
41k ILE* 4.0 26.7 - - + -
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Residues in contact with VAL 109 (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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31d VAL* 4.7 3.7 - - + +
32d LEU* 4.1 18.6 - - + -
42d VAL* 3.5 28.7 - - + -
43d LEU 3.6 2.7 - - - -
44d ILE* 4.2 18.4 - - + -
63d CYS* 5.8 0.9 - - + -
65d MET* 4.8 9.4 - - + -
106d VAL* 3.7 20.2 - - + -
108d VAL* 1.3 80.2 - - - +
110d LEU* 1.3 64.7 + - - +
111d ARG 4.3 0.4 + - - -
61f GLU 4.0 0.2 - - - +
62f VAL* 3.3 6.8 - - - +
63f LEU* 3.0 54.6 + - + +
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Residues in contact with LEU 110 (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 VAL* 3.4 5.8 - - - -
43d LEU* 2.8 42.1 + - + +
109d VAL* 1.3 76.8 - - - +
111d ARG* 1.3 81.6 + - - +
113d PRO* 4.9 0.4 - - + -
59f LEU* 3.8 7.9 - - + +
60f GLY* 3.7 29.2 - - - +
61f GLU 3.4 13.9 - - - +
62f VAL* 3.8 8.5 - - + -
41k ILE* 3.8 27.4 - - + -
45k ILE* 3.9 16.8 - - + -
48k PHE* 3.5 26.1 - - + -
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Residues in contact with ARG 111 (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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31d VAL* 3.5 20.3 - - + +
34d GLN* 2.9 53.9 + - - +
35d SER* 3.0 24.9 - - - +
38d ASN* 4.2 11.1 - - - +
40d THR* 3.6 26.9 + - - +
42d VAL* 4.1 6.0 - - + +
109d VAL 4.3 0.4 - - - -
110d LEU* 1.3 88.5 - - - +
112d ASN* 1.3 67.9 + - - +
113d PRO* 3.1 5.8 - - - +
61f GLU* 3.1 52.4 + - + +
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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