Contacts of the strand formed by residues 100 - 107 (chain B) in PDB entry 4Q29
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 PHE 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B CYS 3.6 0.7 - - - +
40B ILE* 3.3 4.2 - - - -
41B VAL* 2.8 41.8 + - + +
60B VAL* 3.5 38.8 - - + -
62B GLN 3.3 12.8 - - - -
63B GLY* 4.7 0.4 - - - -
64B ASN* 3.5 26.5 - - - +
65B ALA* 3.6 16.6 - - + -
67B ILE* 4.6 3.8 - - + -
76B VAL* 3.6 11.4 - - + -
92B VAL* 3.6 27.8 - - + -
94B ASN* 3.7 22.7 - - + +
98B GLU 3.3 1.2 + - - +
99B ASP* 1.3 72.7 - - - +
101B HIS* 1.3 63.0 + - - +
102B PHE* 3.5 28.4 - + + -
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Residues in contact with HIS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LYS* 4.6 10.0 + - - -
10B TRP* 3.9 13.2 - + - -
38B TRP* 2.9 30.5 + + - +
39B CYS 3.3 3.6 - - - -
40B ILE* 3.6 25.8 - - + +
60B VAL* 3.9 0.5 - - - -
61B ILE* 2.9 37.9 + - + -
62B GLN* 2.9 36.0 + - + +
99B ASP* 3.7 30.1 + - + +
100B PHE* 1.3 82.8 - - - +
102B PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.3 9.0 - - + -
38B TRP* 3.7 1.6 - - - +
39B CYS* 2.8 71.4 + - + +
41B VAL* 4.2 16.6 - - + -
58B PHE* 3.7 46.7 - + + -
59B ILE 3.2 15.0 - - - +
60B VAL* 4.1 8.5 - - + -
61B ILE* 4.1 8.1 - - - +
92B VAL* 3.9 24.7 - - + -
100B PHE* 3.5 26.2 - + + -
101B HIS* 1.3 74.1 - - - +
103B TYR* 1.3 60.8 + - - +
104B THR* 4.3 4.0 - - + -
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Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 5.6 0.8 - - + +
59A ILE* 3.7 34.5 - - + +
81A LEU* 4.2 12.6 - - + +
22B SER 4.8 1.8 + - - -
24B LEU* 3.4 35.2 + - + +
37B ALA* 3.3 25.3 + - - -
38B TRP* 3.4 44.0 - + + -
57B LEU 3.9 0.7 - - - +
58B PHE* 3.5 1.2 - - - -
59B ILE* 2.8 45.7 + - + +
61B ILE* 3.9 12.0 - - + +
102B PHE* 1.3 75.3 - - - +
104B THR* 1.3 74.1 + - - +
105B ILE* 3.5 23.7 + - + -
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Residues in contact with THR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY* 3.1 6.1 - - - -
37B ALA* 2.9 46.7 + - + +
39B CYS* 3.9 12.8 - - - -
56B GLU* 2.5 36.9 + - - +
57B LEU 3.3 5.7 + - - -
58B PHE* 4.0 12.6 - - - -
102B PHE* 4.2 4.2 - - + -
103B TYR* 1.3 76.8 - - - +
105B ILE* 1.3 63.8 + - - +
106B TRP* 3.8 21.2 - - + -
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PHE* 3.7 33.0 - - + -
57A LEU* 5.3 1.1 - - + -
59A ILE* 4.8 0.9 - - + -
105A ILE* 4.0 23.1 - - + -
24B LEU* 5.4 0.4 - - + -
34B PHE* 3.8 30.1 - - + -
35B GLY 3.3 12.1 - - - +
36B GLY* 4.0 1.3 - - - -
56B GLU* 3.2 2.6 - - - +
57B LEU* 2.9 47.4 + - + +
59B ILE* 4.9 3.4 - - + -
103B TYR* 3.5 31.4 - - + -
104B THR* 1.3 75.8 + - - +
106B TRP* 1.3 62.6 + - - +
107B TRP* 3.4 3.1 - - + -
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Residues in contact with TRP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ARG* 3.7 31.6 - - + -
25B LEU* 6.2 1.1 - - + -
34B PHE* 3.2 4.9 - - - +
35B GLY* 2.8 50.4 + - - +
36B GLY* 3.7 35.0 - - - -
37B ALA* 4.0 6.7 - - + -
54B GLU* 3.5 32.1 + - + +
55B TYR 3.1 13.0 - - - +
56B GLU* 4.2 17.5 - - + +
104B THR* 3.8 27.4 - - + -
105B ILE* 1.3 74.7 - - - +
107B TRP* 1.3 64.7 + - - +
111B SER* 5.4 0.2 - - - -
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Residues in contact with TRP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.2 11.2 - - + -
31A ASN 3.1 21.6 + - - -
32A THR* 3.5 20.9 - - + -
33A PRO* 3.3 26.6 - - + +
34A PHE* 3.7 21.8 - + - -
115A PHE* 3.5 20.6 - + - -
33B PRO 3.7 17.9 - - - +
34B PHE* 4.1 4.9 - - + -
54B GLU* 2.9 11.9 - - - +
55B TYR* 2.8 57.3 + + + +
56B GLU 3.9 9.6 - - - -
57B LEU* 3.9 27.4 - - + -
83B ILE* 5.7 0.2 - - + -
105B ILE* 3.4 17.7 - - + -
106B TRP* 1.3 83.4 - - - +
108B ASP* 1.3 59.4 + - - +
111B SER* 3.5 6.3 - - - +
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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