Contacts of the strand formed by residues 22 - 28 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLY 3.4 6.5 - - - +
17A HIS* 3.9 2.9 - - + +
320A MET* 3.4 20.5 - - + +
6B ILE* 4.5 1.1 - - + -
17B MET* 3.8 4.2 - - - +
21B TRP* 1.3 85.9 - - + +
23B GLY* 1.3 58.1 + - - +
36B ALA* 3.6 8.0 - - - +
37B ASP* 2.8 23.4 + - - +
40B SER* 3.2 50.9 - - - +
41B THR* 3.3 3.0 + - - -
44B ALA* 3.5 19.2 - - + +
111B THR* 2.8 47.6 + - - +
114B GLU* 3.5 9.2 - - + +
115B MET* 3.8 32.5 - - + -
118B LEU* 3.8 11.9 - - + -
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.4 8.3 - - - +
16A GLY 3.0 32.2 + - - +
14B TRP* 3.8 6.6 - - - -
17B MET* 3.6 8.4 - - - -
22B TYR* 1.3 76.4 - - - +
24B PHE* 1.3 68.0 - - - -
35B ALA 3.5 10.1 - - - -
37B ASP* 3.6 8.1 - - - -
118B LEU* 4.2 2.7 - - - +
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Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.8 29.8 - - + -
14A CYS 3.4 3.4 - - - -
15A LEU* 3.8 22.7 - - + -
14B TRP* 4.0 1.8 - - - -
17B MET* 4.0 0.6 - - - +
23B GLY* 1.3 76.5 - - - -
25B ARG* 1.3 61.1 + - - +
26B HIS* 5.7 0.9 - - - +
33B GLY 4.8 0.2 - - - -
34B GLN* 3.2 4.9 - - - +
35B ALA 2.8 41.3 + - - +
36B ALA 5.2 0.2 - - - -
37B ASP* 4.0 24.5 - - + -
118B LEU* 3.6 21.3 - - + -
122B THR* 3.7 25.4 - - + -
152B ILE* 5.2 1.8 - - + -
153B ARG* 3.5 53.3 + - + +
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.5 3.7 - - - +
14A CYS* 2.9 37.6 + - + +
325A GLU* 4.5 8.9 + - - -
14B TRP* 3.5 61.1 - - + +
16B GLY* 4.6 8.9 - - - -
24B PHE* 1.3 71.1 - - - +
26B HIS* 1.3 62.9 + - - +
32B THR* 6.0 4.0 - - + -
33B GLY 3.3 8.5 - - - +
34B GLN* 2.7 42.3 + - + +
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Residues in contact with HIS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR 3.1 13.2 - - - +
13A LEU* 4.2 3.8 - - + -
14A CYS* 6.2 0.4 - - - -
24B PHE 5.6 0.6 + - - -
25B ARG* 1.3 77.2 - - - +
27B GLN* 1.3 58.9 + - - +
28B ASN* 3.3 27.1 - - + -
31B GLY 3.1 16.8 + - - -
32B THR* 3.1 8.9 - - - +
33B GLY* 2.7 69.4 + - - -
34B GLN* 5.0 0.2 - - - -
146B ASN* 3.4 15.5 + - - -
149B ILE* 3.8 39.0 - - + +
153B ARG* 4.3 15.1 + - - -
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Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 4.0 2.6 - - - +
12A THR* 3.1 42.5 + - - +
26B HIS* 1.3 72.1 - - - +
28B ASN* 1.3 61.6 + - - +
32B THR* 3.1 35.0 + - - +
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Residues in contact with ASN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR 5.7 0.4 - - - -
11A ALA* 4.9 6.3 - - + +
26B HIS* 3.3 13.0 + - + -
27B GLN* 1.3 79.4 - - - +
29B SER* 1.3 61.9 + - - +
30B GLU* 2.7 18.4 + - - +
31B GLY* 2.8 46.9 + - - +
32B THR* 4.6 0.4 + - - -
144B CYS 3.1 22.2 - - - +
145B ASP* 3.1 18.7 - - - -
146B ASN* 2.6 28.3 + - - -
149B ILE* 4.4 4.5 - - + -
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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