Contacts of the strand formed by residues 15 - 22 (chain B) in PDB entry 4B3E
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 GLN 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.3 13.0 - - - +
9B LYS* 5.0 13.0 + - + +
13B PRO* 3.6 17.8 + - - +
14B VAL* 1.3 76.0 - - - +
16B GLY* 1.3 55.8 + - - +
35B ILE* 3.5 6.2 - - - +
36B LYS* 2.7 68.3 + - + +
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Residues in contact with GLY 16 (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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7B VAL* 3.6 5.2 - - - +
8B LEU* 2.9 40.0 + - - +
15B GLN* 1.3 78.6 - - - +
17B ILE* 1.3 69.8 + - - +
18B ILE 4.3 0.2 - - - -
34B SER 3.3 13.0 - - - -
35B ILE* 4.1 2.5 - - - -
36B LYS* 5.6 1.6 - - - -
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Residues in contact with ILE 17 (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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5B VAL* 4.0 12.8 - - + -
6B CYS 3.3 5.6 - - - +
7B VAL* 4.6 8.5 - - + -
16B GLY* 1.3 79.8 - - - +
18B ILE* 1.3 66.0 + - - +
19B ASN* 4.5 10.9 - - - +
33B GLY* 3.4 5.4 - - - -
34B SER 3.1 28.1 + - - +
54G THR* 3.8 44.4 - - + +
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Residues in contact with ILE 18 (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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5B VAL* 3.3 5.2 - - - +
6B CYS* 2.8 34.9 + - + +
8B LEU* 4.0 16.6 - - + -
17B ILE* 1.3 82.7 - - - +
19B ASN* 1.3 64.4 + - - +
20B PHE* 3.7 15.1 - - + -
31B VAL* 3.6 29.6 - - + -
32B TRP 3.7 1.6 - - - +
33B GLY* 4.1 13.7 - - - +
35B ILE* 4.2 9.0 - - + -
45B PHE* 4.1 7.4 - - + -
97B VAL* 4.0 29.6 - - + -
117B LEU* 3.7 26.9 - - + -
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Residues in contact with ASN 19 (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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4B ALA 3.6 5.0 + - - +
5B VAL* 3.7 21.2 - - - +
17B ILE* 4.5 9.7 - - - +
18B ILE* 1.3 74.1 - - - +
20B PHE* 1.3 67.0 + - - +
31B VAL* 3.3 6.1 - - - -
32B TRP* 2.7 79.3 + - + +
33B GLY* 4.4 5.2 - - - -
54G THR* 5.8 0.4 - - - +
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Residues in contact with PHE 20 (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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3B LYS* 3.2 7.4 - - - +
4B ALA* 2.9 58.9 + - + +
6B CYS* 4.3 7.9 - - + -
18B ILE* 3.7 31.4 - - + -
19B ASN* 1.3 76.0 - - - +
21B GLU* 1.3 60.7 + - - +
29B VAL* 4.0 13.9 - - + -
30B LYS 3.1 5.4 - - - -
31B VAL* 3.9 29.4 - - + -
32B TRP* 4.0 3.9 - - - -
84B LEU* 5.1 6.1 - - + -
104B ILE* 4.7 2.2 - - + -
106B LEU* 4.1 5.4 - - + -
112B ILE* 3.6 27.1 - - + -
117B LEU* 4.0 14.4 - - + -
149B ILE* 4.0 24.7 - - + -
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Residues in contact with GLU 21 (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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1B ALA* 4.3 17.7 - - + -
2B THR 3.5 9.0 - - - +
3B LYS* 4.1 22.4 + - + +
20B PHE* 1.3 74.4 - - - +
22B GLN* 1.3 64.4 + - - +
23B LYS* 3.7 21.7 - - - +
28B PRO 3.9 0.9 - - - +
29B VAL* 3.4 3.4 - - - +
30B LYS* 2.7 60.5 + - + +
32B TRP* 3.7 24.3 - - + -
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Residues in contact with GLN 22 (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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1B ALA* 4.3 1.6 - - - -
2B THR* 3.0 38.8 + - - +
21B GLU* 1.3 74.1 - - - +
23B LYS* 1.3 64.6 + - - +
24B GLU* 3.3 17.8 + - - +
25B SER* 3.4 15.6 + - - -
27B GLY 2.9 20.6 + - - -
28B PRO 3.5 16.8 - - - +
29B VAL* 3.6 16.5 - - + +
104B ILE 4.5 0.6 + - - -
105B SER* 3.1 21.4 + - - +
106B LEU* 2.9 39.6 + - + +
107B SER* 4.0 5.2 + - - -
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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