Contacts of the strand formed by residues 36 - 43 (chain B) in PDB entry 3GCU
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 GLY 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B SER* 3.4 2.1 - - - -
33B GLY 2.8 34.4 + - - +
34B ALA 3.6 0.2 - - - -
35B TYR* 1.3 82.5 - - - +
37B SER* 1.3 61.0 + - - -
53B LYS* 4.7 2.9 - - - -
54B LYS 3.2 14.8 - - - -
55B LEU* 4.3 0.2 - - - -
56B SER* 3.8 7.2 - - - -
171B LEU* 3.7 14.9 + - - +
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Residues in contact with SER 37 (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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16B THR* 4.3 16.2 + - - +
18B TRP* 3.3 25.5 - - - -
31B GLY 3.3 6.5 - - - -
32B SER* 3.7 18.8 - - - +
33B GLY 5.1 0.5 + - - -
36B GLY* 1.3 76.0 - - - -
38B VAL* 1.3 64.6 + - - +
53B LYS* 3.3 4.0 - - - +
54B LYS* 2.9 34.1 + - - +
56B SER* 5.9 0.7 - - - -
171B LEU* 4.7 0.2 - - - -
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Residues in contact with VAL 38 (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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18B TRP* 4.0 0.8 - - - -
29B PRO* 3.6 4.5 - - - +
30B VAL* 2.8 45.5 + - + -
31B GLY 2.7 16.6 + - - +
37B SER* 1.3 80.2 - - - +
39B CYS* 1.3 61.2 + - - +
51B ALA* 3.7 27.6 - - + -
52B VAL 3.2 11.2 - - - +
53B LYS* 3.9 13.9 - - + +
171B LEU* 3.7 28.5 - - + -
401B R48 4.0 23.1 - - + +
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Residues in contact with CYS 39 (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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13B LEU* 3.7 26.7 - - - -
18B TRP* 3.7 28.0 - - + -
27B LEU* 4.0 15.7 - - + -
28B SER 3.2 9.4 - - - +
29B PRO* 3.7 24.5 - - - -
30B VAL* 3.9 2.7 - - - -
38B VAL* 1.3 73.8 - - - +
40B ALA* 1.3 68.6 + - - +
51B ALA* 3.4 1.9 - - - -
52B VAL* 2.8 39.4 + - + +
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Residues in contact with ALA 40 (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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26B ASN 3.6 2.7 - - - +
27B LEU* 3.4 1.4 - - - -
28B SER* 2.8 36.8 + - - +
30B VAL* 3.5 25.6 - - + +
39B CYS* 1.3 75.2 - - - +
41B ALA* 1.3 60.2 + - - +
49B ARG* 3.4 28.3 - - - +
50B VAL 3.4 6.5 - - - -
108B LEU* 3.7 18.2 - - + -
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Residues in contact with ALA 41 (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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24B TYR* 4.2 6.5 - - + -
25B GLN 3.5 12.3 - - - +
26B ASN 4.1 2.9 - - - -
27B LEU* 3.8 21.5 - - + -
40B ALA* 1.3 77.7 - - - +
42B PHE* 1.3 60.7 + - - +
43B ASP 3.9 0.4 - - - -
49B ARG* 3.3 15.2 + - - +
50B VAL* 2.7 48.0 + - + -
52B VAL* 4.1 10.5 - - + -
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Residues in contact with PHE 42 (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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193A ILE 5.6 1.6 - - - -
194A MET* 4.4 16.2 - - - -
195A LEU 5.1 1.8 - - - -
196A ASN* 3.9 41.5 - - + +
228A HIS* 5.4 0.4 - + - -
23B ARG 3.4 0.9 - - - +
24B TYR* 3.4 1.8 - - - -
25B GLN* 2.8 42.2 + - + +
26B ASN* 3.9 22.1 + - + +
41B ALA* 1.3 71.9 - - - +
43B ASP* 1.3 58.9 + - - +
44B THR* 3.3 36.3 + - + -
47B GLY* 3.3 40.2 - - - -
48B LEU 4.0 3.6 - - - -
49B ARG* 4.5 15.7 - - - +
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Residues in contact with ASP 43 (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* 2.9 49.6 + - - -
24B TYR* 3.8 12.8 - - + -
41B ALA 3.9 1.6 + - - -
42B PHE* 1.3 71.7 - - - +
44B THR* 1.3 56.0 + - - +
45B LYS 3.2 5.0 + - - -
46B THR* 2.9 24.6 + - - +
47B GLY* 2.7 34.0 + - - -
48B LEU* 2.9 20.7 + - - +
50B VAL* 3.8 19.8 - - + +
87B LEU* 5.5 1.7 - - - +
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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