Contacts of the strand formed by residues 22 - 28 (chain D) in PDB entry 5HMG
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 TYR 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C GLY 3.4 6.7 - - - +
17C HIS* 3.9 2.9 - - + +
320C MET* 3.4 20.7 - - + +
6D ILE* 4.5 0.9 - - + -
17D MET* 3.9 4.3 - - - -
21D TRP* 1.3 87.0 - - + +
23D GLY* 1.3 58.4 + - - +
36D ALA* 3.6 8.7 - - - +
37D ASP* 2.8 23.3 + - - +
40D SER* 3.1 50.5 - - - +
41D THR* 3.3 3.6 + - - -
44D ALA* 3.5 17.8 - - + +
111D THR* 2.9 46.8 + - - -
114D GLU* 3.5 9.4 - - + +
115D MET* 3.8 32.3 - - + -
118D LEU* 3.8 11.7 - - + -
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Residues in contact with GLY 23 (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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15C LEU* 3.4 8.3 - - - +
16C GLY 2.9 31.9 + - - +
14D TRP* 3.8 6.2 - - - -
17D MET* 3.6 9.2 - - - -
22D TYR* 1.3 76.0 - - - +
24D PHE* 1.3 67.7 + - - -
35D ALA 3.5 10.1 - - - -
37D ASP* 3.6 8.5 - - - -
118D LEU* 4.3 3.6 - - - +
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Residues in contact with PHE 24 (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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13C LEU* 3.8 29.2 - - + -
14C CYS 3.4 2.9 - - - -
15C LEU* 3.8 22.4 - - + -
14D TRP* 3.9 1.3 - - - -
17D MET* 4.0 0.4 - - - +
23D GLY* 1.3 76.3 - - - -
25D ARG* 1.3 62.2 + - - +
26D HIS* 6.0 0.9 - - - +
34D GLN* 3.2 5.2 - - - +
35D ALA 2.8 41.2 + - - +
36D ALA 5.2 0.4 - - - -
37D ASP* 4.1 24.0 - - + -
118D LEU* 3.6 20.0 - - + -
122D THR* 3.7 25.6 - - + -
152D ILE* 5.2 2.2 - - + -
153D ARG* 3.5 54.0 + - + +
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Residues in contact with ARG 25 (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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13C LEU* 3.2 5.5 - - - +
14C CYS* 2.9 35.3 + - + +
14D TRP* 3.5 61.3 - - + +
16D GLY* 4.7 9.9 - - - +
24D PHE* 1.3 71.5 - - - +
26D HIS* 1.3 63.3 + - - +
33D GLY 3.3 7.6 - - - +
34D GLN* 2.7 45.6 + - + +
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Residues in contact with HIS 26 (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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12C THR 3.1 14.1 - - - +
13C LEU* 4.0 11.9 - - + -
14C CYS* 4.9 0.7 - - - +
24D PHE* 6.0 0.6 - - - +
25D ARG* 1.3 77.6 - - - +
27D GLN* 1.3 62.7 + - - +
28D ASN* 3.5 28.4 + - - -
31D GLY 3.8 4.1 + - - -
32D THR* 3.2 6.2 - - - +
33D GLY* 2.8 58.1 + - - -
146D ASN* 3.1 27.3 + - - -
149D ILE* 3.3 32.6 - - + +
153D ARG* 4.1 15.3 + - - -
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Residues in contact with GLN 27 (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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11C ALA* 3.7 3.3 - - - +
12C THR* 3.0 41.0 + - - +
26D HIS* 1.3 75.8 - - - +
28D ASN* 1.3 62.7 + - - +
31D GLY* 3.6 9.2 - - - +
32D THR* 3.4 27.1 - - + +
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Residues in contact with ASN 28 (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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10C THR 5.3 2.0 - - - -
11C ALA* 4.2 10.5 - - + +
26D HIS* 3.5 12.8 + - + -
27D GLN* 1.3 79.1 - - - +
29D SER* 1.4 64.5 + - - +
30D GLU 3.1 15.0 - - - +
31D GLY* 2.9 41.4 + - - -
144D CYS 2.8 18.8 - - - +
145D ASP 2.8 28.3 - - - +
146D ASN* 2.8 24.6 + - - +
149D ILE* 3.5 6.3 - - + +
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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