Contacts of the strand formed by residues 71 - 79 (chain H) 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 PRO 71 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C LYS* 6.1 4.5 - - - +
63H GLU* 4.3 23.8 - - + +
64H ALA 3.4 10.5 - - - +
65H MET* 3.8 21.3 - - + -
69H GLY 4.5 0.7 - - - +
70H SER* 1.3 90.6 + - - +
72H ILE* 1.3 64.2 + - - +
73H LYS* 5.9 0.4 - - - +
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Residues in contact with ILE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62H ALA 3.7 1.0 - - - +
63H GLU* 3.3 4.8 - - - +
64H ALA 2.9 32.5 + - - +
66H ASN* 3.0 40.2 - - + +
70H SER* 5.0 1.1 - - - +
71H PRO* 1.3 78.6 - - - +
73H LYS* 1.3 65.7 + - - +
74H VAL* 3.9 21.9 + - + -
18I LEU* 3.4 31.3 - - + +
19I PHE* 4.0 0.7 - - - -
20I GLY* 4.0 12.3 - - - +
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Residues in contact with LYS 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H GLU* 3.1 41.1 + - - +
62H ALA 3.4 3.8 - - - -
63H GLU* 3.6 23.8 + - + +
71H PRO 6.1 0.2 - - - +
72H ILE* 1.3 76.8 - - - +
74H VAL* 1.3 62.9 + - - +
101H ARG* 3.3 20.4 - - - +
20I GLY* 5.6 1.4 - - - -
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Residues in contact with VAL 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H GLU* 3.2 6.8 - - - -
62H ALA* 2.8 38.6 + - + +
72H ILE* 3.9 10.3 - - + -
73H LYS* 1.3 78.5 - - - +
75H THR* 1.3 63.2 + - - +
76H LEU* 5.0 3.8 - - + -
18I LEU* 3.8 27.6 - - + -
19I PHE 3.5 23.6 - - - +
20I GLY* 3.7 15.0 - - - -
111I ILE 4.3 1.3 - - - +
112I SER* 3.2 33.9 - - - -
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Residues in contact with THR 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H ILE* 3.4 32.9 - - + +
60H VAL 3.6 4.5 - - - +
61H GLU* 4.4 4.4 + - - +
74H VAL* 1.3 74.9 - - - +
76H LEU* 1.3 63.1 + - - +
77H ALA 4.0 10.1 - - - +
78H THR* 4.4 4.5 - - - +
103H LYS* 4.8 6.4 - - - +
46I THR* 3.7 2.6 + - - -
48I SER* 4.3 11.7 + - - +
110I HIS* 3.4 45.5 + - + +
111I ILE 4.9 2.2 + - - -
112I SER* 3.2 21.3 + - - -
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Residues in contact with LEU 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LEU* 3.7 27.4 - - + -
47H VAL* 5.1 3.4 - - + -
60H VAL* 2.7 35.0 + - + +
62H ALA* 4.0 29.4 - - + +
74H VAL* 3.7 3.3 + - + +
75H THR* 1.3 76.6 - - - +
77H ALA* 1.3 62.9 + - + +
89H LEU* 4.0 14.6 - - + +
92H PHE* 3.6 36.8 - - + -
94H ILE* 5.1 1.1 - - + -
100H LEU* 4.3 5.4 - - + -
111H ILE* 4.9 4.9 - - + -
18I LEU* 5.9 0.4 - - + -
46I THR* 2.8 32.1 + - - +
48I SER* 4.0 1.7 + - - -
112I SER* 4.6 2.2 - - - +
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Residues in contact with ALA 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H VAL* 4.4 24.2 - - + -
58H HIS 3.9 0.3 - - - +
59H ILE* 3.4 5.0 - - - +
60H VAL* 3.0 29.2 + - + +
75H THR* 3.7 2.7 - - - +
76H LEU* 1.3 83.0 - - + +
78H THR* 1.3 63.0 + - - +
79H LEU* 4.1 5.2 - - + -
87H VAL* 4.1 31.4 - - + -
89H LEU* 5.1 0.2 - - + -
48I SER* 3.9 6.7 - - - -
86I THR* 4.1 2.7 - - - -
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Residues in contact with THR 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H LEU* 3.6 35.9 - - + -
58H HIS 3.3 5.6 - - - +
59H ILE* 3.6 14.1 - - + +
75H THR* 4.4 1.2 - - - +
77H ALA* 1.3 72.8 + - - +
79H LEU* 1.3 66.0 + - - +
84H GLN* 3.9 8.3 - - - +
48I SER* 3.3 12.1 - - - -
49I LEU 2.9 29.2 + - - +
81I MET* 4.6 0.9 - - - -
85I PRO* 3.9 19.6 - - + +
86I THR* 2.7 32.5 + - - -
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Residues in contact with LEU 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H VAL* 3.6 33.9 - - + +
48H SER* 4.2 2.5 - - - -
49H LEU* 4.0 26.2 - - + +
57H LEU* 3.7 4.2 - - - +
58H HIS* 2.7 40.1 + - + +
60H VAL* 5.2 2.0 - - + -
77H ALA* 4.5 7.9 - - + +
78H THR* 1.3 74.1 - - - +
80H LYS* 1.3 63.8 + - - +
84H GLN 3.4 17.3 - - - +
85H PRO 3.8 11.4 - - - +
87H VAL* 3.4 43.1 - - + +
109H VAL* 4.4 4.0 - - + -
85I PRO* 5.2 1.6 - - - -
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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