Contacts of the strand formed by residues 77 - 82 (chain F) in PDB entry 5JLH
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 GLU 77 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72F ASP* 5.4 0.3 - - - +
73F GLU 3.8 0.5 - - - -
74F GLY* 2.5 36.5 + - - +
75F GLU* 4.4 1.5 - - + +
76F GLU* 1.3 79.8 - - + +
78F ALA* 1.3 59.4 + - - +
79F GLU 4.2 0.2 - - - -
90F ARG* 3.4 40.9 + - + +
91F LEU 3.5 10.3 - - - +
92F PRO* 5.3 3.4 - - + -
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Residues in contact with ALA 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F LEU* 4.5 12.1 - - + -
72F ASP 3.4 14.6 - - - +
73F GLU* 4.1 10.5 - - + +
75F GLU 6.0 0.2 - - - +
76F GLU 3.3 4.4 + - - +
77F GLU* 1.3 74.1 - - - +
79F GLU* 1.3 61.8 - - - +
80F VAL* 3.4 18.6 - - + +
89F LEU 3.4 10.6 - - - +
90F ARG* 3.6 10.1 - - - -
91F LEU 3.3 12.5 + - - +
93F ARG* 5.0 8.1 - - + -
96F ILE* 4.9 8.5 - - + +
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Residues in contact with GLU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F LEU 2.6 26.9 - - - +
71F ARG* 4.8 0.5 - - - +
72F ASP* 3.0 37.1 + - + +
77F GLU 4.2 0.6 - - - -
78F ALA* 1.3 69.3 - - - +
80F VAL* 1.3 55.2 + - - +
81F GLU 4.4 0.2 + - - -
88F ARG* 3.5 56.8 + - + +
89F LEU* 3.5 8.7 - - - +
90F ARG* 4.7 27.8 + - + +
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Residues in contact with VAL 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F VAL* 5.1 1.6 - - + +
58F VAL* 5.4 5.6 - - + -
68F ALA* 3.2 32.8 - - + +
69F ALA 3.0 19.7 - - - +
70F LEU* 3.8 11.4 - - + +
78F ALA* 3.4 26.7 - - + +
79F GLU* 1.3 83.1 - - - +
81F GLU* 1.3 61.4 + - - +
82F LEU* 3.5 7.9 + - + +
87F ARG 3.3 14.6 - - - +
88F ARG* 3.5 8.6 - - - -
89F LEU 3.2 14.3 + - - +
96F ILE* 4.6 17.0 - - + -
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Residues in contact with GLU 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ARG* 4.5 8.5 + - - -
68F ALA* 3.2 0.8 - - - -
69F ALA* 2.5 50.3 + - + +
71F ARG* 3.6 34.5 + - + +
80F VAL* 1.3 70.1 - - - +
82F LEU* 1.3 65.1 + - - +
83F ALA* 3.6 0.9 + - - -
86F GLY* 5.5 5.4 - - - +
87F ARG 4.2 4.7 - - - +
88F ARG* 3.6 36.9 + - + +
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Residues in contact with LEU 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F VAL* 3.6 23.6 - - + -
66F GLU* 3.8 19.7 - - - +
67F ALA 4.0 1.1 - - - +
68F ALA* 3.5 22.7 - - + -
80F VAL* 3.5 7.8 + - + +
81F GLU* 1.3 73.5 - - - +
83F ALA* 1.3 65.5 + - - +
84F GLU* 3.3 1.6 - - + +
85F SER* 4.6 7.9 - - - +
86F GLY* 3.1 28.2 + - - +
87F ARG* 3.6 52.8 + - + +
89F LEU* 4.7 9.0 - - + -
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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