Contacts of the strand formed by residues 29 - 36 (chain B) in PDB entry 4AU8
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 ILE 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 4.0 14.8 - - + -
20B LYS* 3.6 30.7 - - + -
21B ALA 3.4 6.3 - - - +
22B LYS* 3.8 35.9 - - + -
27B HIS 3.4 6.9 + - - +
28B GLU* 1.3 81.3 - - - +
30B VAL* 1.3 66.4 + - - +
67B HIS* 6.0 0.2 + - - -
81B GLU* 5.7 0.2 - - - -
82B PHE* 3.7 31.4 + - + +
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 3.7 35.2 - - + +
20B LYS* 3.6 4.7 - - - -
21B ALA* 2.9 44.4 + - + +
23B ASN* 5.7 0.2 - - + -
28B GLU* 4.2 20.6 - - + +
29B ILE* 1.3 79.8 - - - +
31B ALA* 1.3 63.8 + - - +
32B LEU* 4.7 2.9 - - + -
67B HIS* 4.5 5.2 - - + -
79B VAL* 3.7 24.9 - - + -
80B PHE 3.4 12.8 - - - +
82B PHE* 3.7 13.7 - - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.3 6.7 - - + -
18B VAL* 4.2 5.4 - - + -
19B PHE 3.3 6.5 - - - +
30B VAL* 1.3 74.5 - - - +
32B LEU* 1.3 60.2 + - - +
79B VAL* 3.7 2.8 - - - -
80B PHE* 2.8 35.6 + - + +
81B GLU 3.6 19.5 - - - +
82B PHE* 4.1 4.6 - - + +
1293B Z3R 3.7 33.2 - - + +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 3.6 36.8 - - + +
6B LYS* 4.3 13.9 - - + -
17B THR 3.9 0.9 - - - +
18B VAL* 3.4 6.8 - - - +
19B PHE* 2.7 44.8 + - + +
21B ALA* 3.9 17.0 - - + -
30B VAL* 4.7 3.1 - - + -
31B ALA* 1.3 76.0 - - - +
33B LYS* 1.3 75.4 + - - +
34B ARG* 4.2 25.8 - - + +
77B THR* 3.8 23.1 - - + -
78B LEU 3.3 4.3 - - - +
79B VAL* 4.8 2.7 - - + -
80B PHE* 5.0 0.2 - - - -
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY* 4.4 8.3 - - - -
14B THR* 4.8 0.8 + - - +
15B TYR* 3.4 41.0 - - + +
16B GLY* 5.7 3.1 - - - +
17B THR 4.0 9.6 - - - +
18B VAL* 3.8 19.5 - - + -
32B LEU* 1.3 77.0 - - - +
34B ARG* 1.3 60.8 + - - +
35B VAL* 5.5 0.2 - - + -
51B GLU* 2.8 26.0 + - - +
76B LEU 3.9 0.5 - - - +
77B THR* 3.4 4.2 - - - +
78B LEU* 2.8 44.5 + - + +
80B PHE* 3.8 11.9 - - + -
144B ASP* 2.8 31.7 + - - +
146B GLY 5.6 0.2 - - - +
1293B Z3R 3.8 15.3 - - - -
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Residues in contact with ARG 34 (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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2B GLN 4.4 17.3 - - - +
4B TYR* 4.4 20.4 + - - +
6B LYS* 3.5 41.9 - - - +
16B GLY* 6.0 2.1 - - - -
17B THR 4.6 6.1 + - - +
19B PHE* 5.4 4.1 - - + -
32B LEU* 4.2 19.8 - - + +
33B LYS* 1.3 73.6 - - - +
35B VAL* 1.3 66.3 + - - +
36B ARG 4.4 0.3 + - - -
70B LEU* 5.3 2.6 - - - +
75B LYS* 4.0 34.6 - - + +
76B LEU 3.4 3.8 - - - +
77B THR* 2.8 40.5 + - - +
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 3.6 38.8 - - + +
33B LYS* 5.3 0.4 - - + -
34B ARG* 1.3 79.3 - - - +
36B ARG* 1.3 76.9 + - - +
37B LEU* 3.6 1.2 + - + +
44B VAL* 3.8 21.1 - - + -
45B PRO* 3.8 20.9 - - + -
48B ALA* 4.1 8.3 - - + -
75B LYS* 3.3 5.3 - - - -
76B LEU* 2.8 53.7 + - + +
78B LEU* 5.1 3.4 - - + -
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Residues in contact with ARG 36 (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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34B ARG 4.4 0.4 + - - -
35B VAL* 1.3 81.1 - - - +
37B LEU* 1.3 64.5 + - - +
44B VAL* 5.2 3.0 - - - +
45B PRO* 4.5 8.8 - - - +
74B LYS 3.9 8.7 + - - +
75B LYS* 3.8 40.9 - - + +
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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
------------------------------------------------------------
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