Contacts of the strand formed by residues 42 - 48 (chain C) in PDB entry 5GJQ
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 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C LYS* 3.6 0.5 - - - -
39C ALA* 2.6 40.5 + - - +
40C ALA 3.4 2.4 + - - -
41C ASN* 1.3 81.7 + - - +
43C VAL* 1.3 62.1 + - - +
143C PRO* 4.2 7.8 - - - +
183C LEU* 4.6 11.0 - - - -
212C CYS 3.3 13.5 - - - -
213C ASN* 4.3 2.5 - - - -
214C GLU* 5.3 0.9 - - - -
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Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE 3.4 18.2 - - - +
38C LYS* 4.0 4.9 - - - -
42C GLY* 1.3 78.1 - - - +
44C VAL* 1.3 74.6 + - - +
45C LEU* 4.9 0.2 - - + -
136C CYS* 3.7 26.9 - - + -
137C GLY 4.3 3.6 - - - +
143C PRO* 3.5 23.3 - - + -
144C TYR 3.9 18.8 - - - +
145C LEU* 4.4 11.7 - - + -
183C LEU* 5.2 1.5 - - - +
211C ILE* 3.4 6.4 - - - +
212C CYS* 2.9 42.0 + - + +
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C VAL 3.8 0.6 - - - +
36C GLY* 3.2 5.7 - - - -
37C ILE* 2.8 37.9 + - + +
42C GLY 5.6 0.4 - - - -
43C VAL* 1.3 78.8 - - - +
45C LEU* 1.3 69.6 + - - +
46C ALA* 4.8 0.4 - - + +
183C LEU* 3.9 8.3 - - + +
186C ALA* 3.7 17.7 - - + +
187C ILE* 3.6 40.4 - - + +
190C ALA* 4.1 20.4 - - + -
209C VAL* 3.9 24.9 - - + -
210C GLY 3.6 3.6 - - - +
211C ILE* 5.1 2.0 - - + -
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C VAL 3.5 1.1 - - - -
36C GLY* 3.9 14.6 - - - -
43C VAL* 4.9 0.4 - - + -
44C VAL* 1.3 83.7 - - - +
46C ALA* 1.3 64.5 + - - +
64C VAL* 4.5 6.2 - - + +
72C GLY* 4.0 18.4 - - - +
73C LEU 4.1 4.0 - - - +
74C VAL* 3.7 36.3 - - + -
134C LEU* 4.0 9.0 - - + +
136C CYS* 3.6 34.3 - - + -
145C LEU* 4.0 20.2 - - + -
209C VAL* 3.4 2.9 - - - +
210C GLY 2.9 35.8 + - - +
217C PHE* 4.7 3.6 - - + -
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Residues in contact with ALA 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C SER* 3.2 5.2 - - - -
35C VAL* 2.9 38.4 + - + +
45C LEU* 1.3 77.3 - - - +
47C THR* 1.3 62.5 + - - +
64C VAL* 5.4 0.4 - - - -
74C VAL* 5.0 3.2 - - - +
190C ALA* 4.7 22.0 - - + +
191C ILE* 6.0 1.8 - - + -
194C LEU* 5.8 6.7 - - + -
207C ILE* 5.9 2.7 - - + -
208C GLU 3.3 10.3 - - - +
209C VAL* 4.1 17.9 - - + -
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Residues in contact with THR 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C PRO 3.1 6.7 + - - -
34C SER* 2.8 25.1 + - - -
46C ALA* 1.3 75.1 - - - +
48C GLU* 1.3 62.6 + - - +
63C LYS* 2.8 54.5 + - + -
64C VAL* 4.2 10.3 - - + -
74C VAL* 4.4 6.3 - - + -
194C LEU* 6.1 4.7 - - - -
207C ILE* 3.2 8.5 - - - +
208C GLU* 2.9 44.0 + - + +
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ALA* 3.5 12.9 - - + +
33C PRO* 3.3 40.1 + - + +
47C THR* 1.3 75.2 + - - +
49C LYS* 1.3 58.6 + - - +
50C LYS* 3.4 43.2 + - + +
63C LYS* 3.3 19.0 + - - +
194C LEU* 5.2 3.9 - - + +
197C SER* 4.9 1.7 - - - +
198C PHE* 4.1 32.3 + - + +
199C GLU 5.1 0.2 + - - -
206C ASN 3.8 6.3 - - - +
207C ILE* 4.4 7.4 - - + +
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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