Contacts of the strand formed by residues 56 - 62 (chain L) 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 ILE 56 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55L GLN* 1.3 75.0 - - - +
57L VAL* 1.3 71.7 + - - +
73L ALA* 5.0 4.5 - - + -
75L ASN* 4.3 16.8 - - - +
79L TYR* 6.3 0.7 - - + -
99L ALA* 3.0 3.3 - - - -
100L LEU* 2.0 60.1 + - + +
101L ASP 3.4 23.5 - - - +
102L MET* 3.9 11.1 - - + +
105L LEU* 4.4 11.4 - - + -
131M THR 4.8 0.2 - - - +
132M TYR* 2.7 47.3 - - + +
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Residues in contact with VAL 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L ILE* 1.3 85.7 - - - +
58L GLY* 1.3 61.5 + - - +
74L THR* 2.3 42.5 + - + +
75L ASN 4.6 0.2 + - - -
97L ARG* 3.4 35.4 - - - +
98L VAL 3.3 8.3 - - - +
100L LEU* 3.6 4.5 - - - +
111L LEU* 5.0 1.8 - - + -
123M VAL* 3.9 8.5 - - + -
131M THR* 3.1 22.1 + - - +
132M TYR* 3.5 1.1 - - - +
133M PHE* 3.1 38.6 - - + +
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Residues in contact with GLY 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L VAL* 1.3 76.4 - - - +
59L GLU* 1.3 55.8 + - - -
72L LYS 4.0 3.1 - - - -
74L THR* 2.7 22.2 - - - -
97L ARG* 4.0 2.5 - - - -
98L VAL* 2.3 52.9 + - - +
100L LEU* 3.5 12.8 - - - +
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Residues in contact with GLU 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L GLY* 1.3 74.6 - - - -
60L VAL* 1.3 64.6 + - - +
61L LEU* 3.2 6.9 + - + +
71L VAL* 3.6 5.0 - - - +
72L LYS* 3.5 44.3 + - - +
74L THR* 3.6 6.2 - - + +
95L GLY* 3.0 36.1 - - - +
96L THR 3.0 3.1 - - - +
97L ARG* 3.6 20.9 + - + +
98L VAL* 4.7 0.2 - - - -
113L ARG* 5.1 10.0 + - - -
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Residues in contact with VAL 60 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59L GLU* 1.3 70.3 - - - +
61L LEU* 1.3 57.1 + - - +
62L LYS* 3.2 35.4 - - - +
63L GLN* 4.2 0.4 - - - +
69L PHE* 4.3 14.1 - - + -
70L ILE 3.9 3.6 - - - +
71L VAL* 4.4 7.2 - - + +
92L LEU* 4.5 9.0 - - + -
93L LYS 3.1 30.5 - - - +
94L PRO 3.2 0.2 - - - -
95L GLY* 2.3 37.4 + - - -
96L THR* 2.6 22.2 + - + +
98L VAL* 3.9 22.4 - - + -
107L ILE* 5.3 1.8 - - + -
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Residues in contact with LEU 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147K ALA* 4.7 12.9 - - - -
148K ASP* 3.0 41.1 - - + +
152K MET* 6.1 0.2 - - - +
59L GLU* 3.2 6.0 + - + +
60L VAL* 1.3 73.7 - - - +
62L LYS* 1.3 64.7 + - + +
70L ILE* 2.6 27.8 + - + +
72L LYS* 3.4 25.6 - - + +
78L ARG* 2.6 53.8 - - + +
94L PRO* 3.6 13.3 - - - +
95L GLY 4.3 1.0 + - - +
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Residues in contact with LYS 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144K PRO* 6.2 2.6 - - - +
145K PRO 4.8 5.8 + - - +
146K GLU* 3.7 23.5 + - + +
147K ALA 5.0 2.0 - - - +
60L VAL* 3.2 17.0 - - - +
61L LEU* 1.3 80.3 - - + +
63L GLN* 1.3 73.4 + - - +
64L LEU* 4.4 12.5 + - - +
69L PHE* 3.5 1.2 - - - -
70L ILE* 2.7 64.7 + - + +
94L PRO* 4.6 8.7 - - + -
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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