Contacts of the strand formed by residues 109 - 117 (chain D) 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 VAL 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D GLU* 3.5 0.9 - - - -
23D LEU* 2.7 43.3 + - + +
47D VAL* 3.5 31.0 - - + -
48D SER 3.5 10.5 - - - +
49D LEU* 3.7 11.0 - - + -
58D HIS* 3.5 35.9 - - + -
60D VAL* 3.8 11.9 - - + -
79D LEU* 4.6 3.1 - - + -
102D LEU* 3.8 22.4 - - + -
108D PRO* 1.3 75.8 - - - +
110D HIS* 1.3 65.0 + - - +
111D ILE* 5.0 2.7 - - + -
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Residues in contact with HIS 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LYS* 4.8 13.5 + - - -
75C THR* 3.5 36.5 + - - +
103C LYS* 3.8 18.2 + - - -
21D CYS 3.5 6.3 - - - +
22D GLU* 3.3 40.3 + - + -
46D THR 3.8 0.4 - - - +
47D VAL* 3.4 5.9 - - - +
48D SER* 2.8 37.5 + - - +
49D LEU 4.5 0.4 - - - -
50D GLY* 3.7 31.0 + - - -
108D PRO* 4.2 6.7 - - + -
109D VAL* 1.3 73.9 - - - +
111D ILE* 1.3 64.6 + - - +
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C VAL* 4.1 2.9 - - - +
75C THR 5.0 1.8 - - - -
19D PHE* 4.1 8.1 - - + -
20D GLY* 3.1 5.4 - - - -
21D CYS* 2.9 41.9 + - - +
23D LEU* 3.7 27.8 - - + -
44D LEU* 3.7 31.2 - - + -
46D THR 3.4 7.9 - - - +
47D VAL* 4.5 16.8 - - + -
60D VAL* 4.0 15.3 - - + -
76D LEU* 5.2 2.9 - - + -
100D LEU* 3.6 25.4 - - + -
109D VAL* 4.8 1.1 - - + +
110D HIS* 1.3 80.7 - - - +
112D SER* 1.3 63.6 + - - +
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Residues in contact with SER 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C VAL* 3.2 24.5 - - - -
75C THR 3.3 14.3 + - - -
76C LEU* 4.5 1.4 - - - -
92C PHE* 3.4 19.8 - - - -
19D PHE* 3.4 7.0 - - - -
44D LEU* 3.8 2.3 - - - -
45D ARG 2.8 21.3 + - - -
46D THR* 2.7 34.2 + - - +
111D ILE* 1.3 79.0 - - - +
113D GLY* 1.3 59.9 + - - +
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Residues in contact with GLY 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C PHE* 3.5 18.9 - - - -
18D LEU* 3.7 2.6 - - - +
19D PHE* 2.9 36.1 + - - +
43D SER 3.1 13.5 - - - -
44D LEU* 4.2 0.4 - - - -
45D ARG* 3.8 5.4 - - - -
112D SER* 1.3 77.8 - - - +
114D GLN* 1.3 65.4 + - - -
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Residues in contact with GLN 114 (chain D).
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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91C GLY 4.4 2.0 + - - -
92C PHE* 3.4 18.7 - - + -
93C GLU* 3.0 42.4 + - - +
16D ASN* 3.3 26.1 + - - +
17D TYR 3.4 3.8 - - - +
18D LEU* 5.4 0.7 - - + -
19D PHE* 4.0 4.0 - - - +
41D GLN 3.7 0.9 - - - +
42D LEU* 3.6 5.9 - - - +
43D SER* 2.8 46.1 + - - +
45D ARG* 3.8 18.9 + - + +
113D GLY* 1.3 78.5 - - - -
115D HIS* 1.3 58.5 + - - +
116D LEU* 3.7 20.0 - - + +
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Residues in contact with HIS 115 (chain D).
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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67C TYR* 3.1 44.7 - + + +
68C GLU* 4.3 3.8 + - - -
16D ASN* 3.7 1.2 - - - -
17D TYR* 2.7 49.8 + - + +
18D LEU 4.9 1.8 - - - +
19D PHE* 4.0 12.0 - - + +
31D PHE* 3.6 35.8 - + + -
32D LYS 6.0 0.2 - - - -
33D VAL* 5.0 4.5 - - + -
40D HIS* 2.8 30.6 + + + +
41D GLN 3.6 5.6 - - - -
42D LEU* 4.9 1.3 - - - -
114D GLN* 1.3 71.4 - - - +
116D LEU* 1.3 73.9 + - - +
117D VAL* 4.1 2.7 - - + +
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D PRO* 5.0 8.7 - - + +
15D GLN 3.3 3.4 - - - +
16D ASN* 3.4 42.6 - - + +
39D GLU 3.8 0.2 - - - +
40D HIS* 3.1 6.8 - - - -
41D GLN* 2.8 55.2 + - + +
43D SER* 3.9 24.5 - - - +
93D GLU* 5.0 7.0 - - + +
114D GLN* 3.7 15.7 - - + +
115D HIS* 1.3 74.3 - - - +
117D VAL* 1.3 65.1 + - - +
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Residues in contact with VAL 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C TYR* 4.3 9.2 - - + -
14D PRO* 3.3 2.7 - - - -
15D GLN* 2.7 45.9 + - + +
17D TYR* 4.0 20.9 - - + -
38D ASN* 3.6 25.8 - - + +
39D GLU 3.4 6.3 - - - +
40D HIS* 3.5 33.7 - - + +
115D HIS* 4.1 7.4 - - + +
116D LEU* 1.3 78.4 - - - +
118D ALA* 1.3 63.5 + - - +
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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