Contacts of the helix formed by residues 21 - 30 (chain H) in PDB entry 5T0J
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 GLN 21 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7G ALA 5.6 3.6 + - - -
8G GLY* 6.1 2.4 - - - -
13G ILE* 5.6 1.6 - - - +
15G ILE* 3.4 32.9 - - + +
16G PHE 5.7 0.4 - - - -
4H ARG* 6.4 0.4 - - - -
12H THR* 3.5 30.5 - - + +
13H PHE* 4.3 23.7 - - + -
20H VAL* 1.3 84.6 - - - +
22H ILE* 1.3 57.8 + - + +
23H GLU 2.6 3.1 + - - -
24H TYR* 2.4 53.5 + - - +
129H PRO* 5.5 0.9 - - - -
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Residues in contact with ILE 22 (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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10H LEU 5.5 0.9 - - - +
11H THR* 4.1 24.0 - - + -
12H THR* 4.3 14.8 - - + +
19H LEU* 3.9 11.0 - - + -
20H VAL 2.9 2.6 + - - -
21H GLN* 1.3 80.5 - - + +
23H GLU* 1.3 50.4 + - - +
24H TYR 3.1 0.4 - - - -
25H ALA* 2.9 12.1 + - + +
26H LEU* 2.7 43.1 + - + +
122H THR 5.1 11.4 - - - +
123H GLN 5.1 2.9 - - - +
124H SER 5.8 1.8 - - - +
125H GLY* 6.1 3.1 - - - -
127H VAL 6.0 1.3 - - - +
129H PRO* 3.6 38.3 - - + +
130H PHE 5.1 6.1 - - - +
151H PRO* 5.4 4.0 - - + -
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Residues in contact with GLU 23 (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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18H LYS* 5.3 7.8 - - + +
19H LEU* 3.0 28.5 + - - +
20H VAL* 3.7 20.5 + - - +
21H GLN 2.6 5.9 + - - +
22H ILE* 1.3 73.7 - - - +
24H TYR* 1.3 67.4 + - + +
26H LEU* 3.0 22.4 + - + +
27H ALA* 2.9 25.8 + - - +
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Residues in contact with TYR 24 (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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7G ALA* 6.3 2.5 - - + -
15G ILE* 5.3 2.2 - - + -
16G PHE* 3.6 16.4 - - - +
17G SER 3.1 17.5 - - - +
18G PRO* 3.5 46.8 - - + +
20G GLY* 3.7 10.9 - - - -
20H VAL* 3.5 30.5 - - + +
21H GLN* 2.4 44.0 + - - +
23H GLU* 1.3 78.9 - - + +
25H ALA* 1.3 59.0 + - - +
27H ALA* 3.2 18.4 + - + +
28H ALA 3.2 8.1 + - - -
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Residues in contact with ALA 25 (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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16G PHE* 3.5 33.4 - - + +
21H GLN 3.8 0.6 + - - -
22H ILE* 2.9 16.5 + - + +
24H TYR* 1.3 76.0 - - - +
26H LEU* 1.3 61.0 + - + +
28H ALA* 3.0 21.0 + - - +
29H VAL* 3.0 17.5 + - - +
79H MET* 5.6 0.2 - - + -
129H PRO* 3.6 21.3 - - + +
130H PHE 4.9 7.4 - - - +
131H GLY* 4.4 3.7 - - - -
151H PRO* 6.1 0.2 - - - -
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Residues in contact with LEU 26 (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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18H LYS* 6.2 4.3 - - + -
19H LEU* 5.6 6.3 - - + +
22H ILE* 2.7 24.5 + - + +
23H GLU* 3.0 28.2 + - + +
25H ALA* 1.3 74.6 - - - +
27H ALA* 1.3 59.4 + - - +
29H VAL* 3.0 22.2 + - + +
30H ALA* 3.4 6.6 + - - +
150H ASP* 6.0 0.4 - - + -
151H PRO* 3.9 35.4 - - + -
152H SER* 4.5 17.0 - - - +
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Residues in contact with ALA 27 (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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18G PRO 3.9 19.3 - - - +
19G GLU 5.0 3.0 - - - +
20G GLY* 4.8 3.6 - - - +
23H GLU 2.9 11.5 + - - +
24H TYR* 3.4 12.8 - - + +
25H ALA 3.2 0.4 - - - -
26H LEU* 1.3 76.9 - - - +
28H ALA* 1.3 59.9 + - - +
30H ALA* 3.6 9.1 + - - +
31H GLY* 3.6 12.6 + - - -
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Residues in contact with ALA 28 (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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16G PHE* 4.9 3.4 - - + -
19G GLU 5.4 0.7 - - - -
20G GLY* 3.8 29.1 - - - +
24H TYR 3.2 5.3 + - - +
25H ALA* 3.0 14.8 + - - +
27H ALA* 1.3 76.7 - - - +
29H VAL* 1.3 63.2 + - - +
30H ALA 3.3 0.2 - - - -
31H GLY* 3.1 13.2 + - - +
32H GLY* 3.2 10.2 + - - -
79H MET* 4.0 26.6 + - + +
131H GLY 5.1 0.2 - - - +
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Residues in contact with VAL 29 (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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25H ALA 3.0 14.3 + - - +
26H LEU* 3.0 18.5 + - + +
28H ALA* 1.3 77.4 - - - +
30H ALA* 1.3 61.3 + - - +
32H GLY* 3.1 14.1 + - - +
77H SER* 4.3 4.0 - - - +
78H GLY* 4.3 5.3 + - - -
131H GLY* 3.2 28.5 - - - +
133H SER* 4.1 24.0 - - - +
151H PRO* 3.7 22.9 - - + -
164H GLY* 4.3 9.5 + - - +
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Residues in contact with ALA 30 (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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26H LEU 3.4 7.0 + - - +
27H ALA* 3.9 10.3 - - - +
28H ALA 3.3 0.4 - - - -
29H VAL* 1.3 79.1 - - - +
31H GLY* 1.3 57.3 + - - +
32H GLY 3.2 1.4 + - - -
164H GLY* 3.7 26.1 - - - +
165H LYS* 4.2 8.1 + - - +
167H TYR* 4.4 32.2 - - + +
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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