Contacts of the strand formed by residues 43 - 48 (chain i) 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 VAL 43 (chain i).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37i ILE 3.4 18.8 - - - +
38i LYS* 4.1 5.4 - - - -
42i GLY* 1.3 77.1 - - - +
44i VAL* 1.3 71.2 + - - +
136i CYS* 3.6 29.2 - - + -
137i GLY 4.4 3.4 - - - +
143i PRO* 3.7 20.0 - - + -
144i TYR 3.9 15.0 - - - +
145i LEU* 4.2 17.7 - - + -
183i LEU* 4.0 3.0 - - - +
211i ILE* 3.3 6.2 - - - +
212i CYS* 2.8 42.1 + - + +
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Residues in contact with VAL 44 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35i VAL 3.9 0.5 - - - +
36i GLY* 3.3 3.6 - - - -
37i ILE 2.9 34.2 + - - +
43i VAL* 1.3 73.1 - - - +
45i LEU* 1.3 69.3 + - - +
46i ALA* 4.9 0.2 - - + -
183i LEU* 2.9 34.5 - - + -
186i ALA* 3.7 17.5 - - + +
187i ILE* 3.5 22.2 - - + +
190i ALA* 4.0 24.5 - - + +
209i VAL* 3.8 24.5 - - + -
210i GLY 3.5 4.5 - - - +
211i ILE* 4.7 1.3 - - + -
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Residues in contact with LEU 45 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35i VAL 3.5 1.6 - - - -
36i GLY* 3.9 8.5 - - - -
43i VAL* 4.9 0.2 - - + -
44i VAL* 1.3 82.6 - - - +
46i ALA* 1.3 64.1 + - - +
64i VAL* 4.9 2.1 - - + +
72i GLY 3.9 17.9 - - - +
73i LEU 4.1 3.6 - - - +
74i VAL* 3.8 33.2 - - + -
134i LEU* 4.0 11.7 - - + +
136i CYS* 3.6 33.4 - - + -
145i LEU* 3.9 27.1 - - + -
209i VAL* 3.4 2.8 - - - +
210i GLY 2.9 38.4 + - - +
217i PHE* 4.6 5.8 - - + -
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Residues in contact with ALA 46 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34i SER* 3.2 4.8 - - - -
35i VAL* 2.9 36.9 + - + +
45i LEU* 1.3 78.4 - - - +
47i THR* 1.3 62.1 + - - +
74i VAL* 4.7 4.8 - - - +
190i ALA* 4.7 17.7 - - + +
191i ILE* 5.5 3.4 - - + -
194i LEU* 3.9 16.4 - - + +
207i ILE* 5.9 0.4 - - + -
208i GLU 3.2 10.8 - - - +
209i VAL* 4.2 16.8 - - + -
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Residues in contact with THR 47 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33i PRO 3.1 8.7 + - - -
34i SER* 2.8 23.8 + - - -
46i ALA* 1.3 76.7 - - - +
48i GLU* 1.3 65.7 + - - +
49i LYS 3.2 1.3 + - - +
63i LYS* 3.0 52.0 + - + -
74i VAL* 4.3 14.1 - - + -
75i TYR 4.9 0.4 - - - -
194i LEU* 3.5 7.0 - - - -
207i ILE* 3.3 6.1 - - - +
208i GLU* 3.0 41.5 + - + +
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Residues in contact with GLU 48 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418K LYS* 5.0 7.4 + - - -
32i ALA* 3.6 11.2 - - + +
33i PRO* 3.2 41.6 + - + +
47i THR* 1.3 75.3 + - - +
49i LYS* 1.3 59.0 + - - +
50i LYS* 3.3 29.8 + - + +
63i LYS* 3.2 19.4 + - - +
194i LEU* 3.9 9.2 - - + +
197i SER* 5.0 1.7 - - - +
198i PHE* 3.5 41.5 + - + +
199i GLU 5.8 0.2 - - - -
206i ASN 3.8 2.9 - - - -
207i ILE* 4.6 2.0 - - + -
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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