Contacts of the strand formed by residues 58 - 65 (chain F) in PDB entry 5EHD
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 HIS 58 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49F LEU* 3.6 30.3 - - + +
53F ALA* 4.2 3.1 - - + +
54F LYS 3.8 12.5 + - - -
56F GLU* 2.9 41.1 + - + +
57F LEU* 1.3 73.2 - - - +
59F ILE* 1.3 65.1 + - - +
60F VAL* 5.3 1.8 - - + -
77F ALA 3.7 0.7 - - - +
78F THR* 3.2 6.2 - - - +
79F LEU* 2.8 46.8 + - + +
102F LEU* 4.3 2.6 - - + +
104F CYS 3.4 4.4 + - - +
105F GLY* 3.7 7.8 - - - -
106F SER 3.5 9.9 - - - -
107F GLY* 2.9 41.3 + - - -
109F VAL* 3.7 15.3 - - + +
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Residues in contact with ILE 59 (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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57F LEU* 4.9 2.5 - - + -
58F HIS* 1.3 78.4 - - - +
60F VAL* 1.3 62.2 + - - +
61F GLU* 5.4 0.4 - - + -
75F THR* 3.6 27.6 - - + +
77F ALA 3.4 2.2 - - - -
78F THR* 3.9 16.4 - - + +
102F LEU* 3.5 5.9 - - - +
103F LYS* 2.7 66.2 + - + -
104F CYS* 3.1 20.2 + - - +
49G LEU 4.4 0.4 - - - +
50G GLY* 4.2 8.1 - - - -
51G ALA* 3.5 41.5 - - + +
110G HIS* 5.7 1.1 - - + -
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Residues in contact with VAL 60 (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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23F LEU* 4.1 15.0 - - + -
47F VAL* 3.7 18.8 - - + -
58F HIS* 5.3 1.8 - - + -
59F ILE* 1.3 77.9 - - - +
61F GLU* 1.3 63.8 + - - +
75F THR* 3.6 6.1 - - - +
76F LEU* 2.8 44.4 + - + -
77F ALA 3.0 17.7 + - - +
79F LEU* 5.0 4.5 - - + -
100F LEU* 5.6 0.9 - - + -
101F ARG 3.6 9.2 - - - +
102F LEU* 3.8 10.5 - - + -
109F VAL* 3.6 30.1 - - + -
111F ILE* 4.5 5.8 - - + -
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Residues in contact with GLU 61 (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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59F ILE* 4.1 0.4 + - + -
60F VAL* 1.3 76.7 - - - +
62F ALA* 1.3 58.7 + - - +
73F LYS* 3.2 44.4 - - - +
74F VAL 3.0 18.2 + - - +
75F THR* 4.4 3.4 + - - +
76F LEU* 4.2 3.8 - - - +
99F VAL 3.9 0.3 - - - +
100F LEU* 3.4 6.2 - - - +
101F ARG* 2.8 68.1 + - + +
103F LYS* 4.3 35.4 + - + +
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Residues in contact with ALA 62 (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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61F GLU* 1.3 75.8 - - - +
63F GLU* 1.3 61.0 + - - +
72F ILE 3.5 2.3 - - - +
73F LYS* 3.6 0.8 - - - -
74F VAL* 2.8 36.1 + - + +
76F LEU* 4.0 16.7 - - + +
94F ILE* 4.2 20.4 - - + -
98F VAL* 4.2 3.6 - - + -
99F VAL 3.1 5.6 - - - +
100F LEU* 3.7 20.2 - - + -
18G LEU* 3.9 6.8 - - + +
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Residues in contact with GLU 63 (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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62F ALA* 1.3 74.7 - - - +
64F ALA* 1.3 64.7 + - - +
71F PRO* 4.4 17.4 - - + +
72F ILE 3.2 15.4 - - - +
73F LYS* 3.2 33.7 + - + +
97F PRO 3.9 0.7 - - - +
98F VAL* 3.4 4.1 - - - -
99F VAL* 2.8 50.6 + - + +
101F ARG* 3.5 31.3 + - - +
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Residues in contact with ALA 64 (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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63F GLU* 1.3 77.8 - - - +
65F MET* 1.3 68.7 + - - +
66F ASN 3.5 0.2 + - - -
71F PRO* 4.2 4.9 - - - -
72F ILE* 3.0 31.3 + - - +
94F ILE* 3.8 22.0 - - + -
95F THR 4.1 5.8 - - - +
97F PRO 3.7 17.5 - - - +
98F VAL* 4.2 2.0 - - + -
18G LEU* 3.6 19.9 - - + +
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Residues in contact with MET 65 (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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64F ALA* 1.3 77.8 - - - +
66F ASN* 1.3 63.8 + - - +
69F GLY* 3.6 32.3 - - - +
70F SER 3.6 1.3 - - - -
71F PRO* 3.9 25.6 - - + -
95F THR 5.3 0.8 + - - -
97F PRO* 4.7 26.3 + - + +
17G TYR* 4.0 10.3 - - + +
18G LEU* 3.3 20.4 + - - +
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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