Contacts of the helix formed by residues 22 - 29 (chain B) in PDB entry 1SVU
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 GLY 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ASP* 3.5 4.5 - - - -
19B ALA 3.0 5.8 + - - -
20B GLY 2.8 8.3 + - - -
21B LEU* 1.3 80.3 - - - +
23B GLY* 1.3 67.5 + - - +
24B PHE 3.1 3.4 + - - -
25B ARG 3.2 9.4 + - - -
26B LEU* 3.3 8.5 + - - +
49B TYR* 3.2 28.9 - - - -
53B PHE* 3.4 11.7 - - - -
285B TYR* 5.5 0.2 - - - -
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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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19B ALA 3.6 1.0 + - - -
21B LEU 3.2 2.8 - - - -
22B GLY* 1.3 77.1 - - - +
24B PHE* 1.3 65.4 + - - +
26B LEU* 3.1 14.0 + - - +
27B ALA 3.6 2.4 + - - -
285B TYR* 3.6 16.3 + - - -
305B SER* 4.0 0.4 - - - -
306B VAL* 4.6 0.4 - - - -
308B ILE* 3.5 18.2 - - - +
311B LEU* 3.7 10.5 - - - +
402B SAH 3.5 20.8 + - - -
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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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14B PHE* 5.6 0.2 - - + -
16B ASP* 3.4 20.9 - - - +
17B LEU 5.0 0.2 - - - -
22B GLY 3.2 0.6 - - - -
23B GLY* 1.3 69.5 - - - +
25B ARG* 1.3 54.2 + - - +
26B LEU 2.5 17.2 + - - -
27B ALA* 2.6 17.9 + - + +
28B LEU* 3.2 14.1 + - + +
76B CYS* 3.2 31.9 - - + -
77B ALA* 3.2 15.9 - - - -
78B GLY* 3.1 36.3 - - - -
117B PHE* 4.0 23.8 - + - -
118B MET* 4.5 0.4 - - - -
119B GLU* 4.4 16.2 - - + -
306B VAL* 5.2 2.2 - - + -
311B LEU* 3.4 39.3 - - + +
402B SAH 4.3 12.5 + - - -
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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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14B PHE* 3.0 31.3 - - + -
16B ASP* 3.0 19.8 + - - +
22B GLY 3.2 5.1 + - - +
24B PHE* 1.3 75.1 - - - +
26B LEU* 1.3 57.1 + - - +
29B GLU* 2.8 65.2 + - - +
35B CYS* 3.5 19.8 + - - +
49B TYR* 2.9 18.5 + - - +
53B PHE* 3.3 50.7 + - - +
55B GLU* 2.7 45.9 + - - +
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Residues in contact with LEU 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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1B MET* 2.9 24.2 - - + +
22B GLY 3.3 8.3 + - - +
23B GLY* 3.1 12.7 + - - +
24B PHE 2.5 7.1 + - - -
25B ARG* 1.3 75.4 - - - +
27B ALA* 1.3 52.3 + - - +
29B GLU* 4.2 3.5 - - - +
30B SER* 2.6 27.4 + - - -
53B PHE* 4.6 14.8 - - + -
285B TYR* 5.8 4.5 - - + -
289B TYR* 5.9 2.9 - - + -
308B ILE* 4.6 10.1 - - + -
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Residues in contact with ALA 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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1B MET* 4.3 0.9 - - - -
4B ILE* 4.0 0.2 - - - +
23B GLY 3.6 3.5 + - - +
24B PHE 2.6 14.3 + - - +
26B LEU* 1.3 70.6 - - - +
28B LEU* 1.3 62.2 + - + +
29B GLU 3.2 0.2 - - - -
30B SER* 2.4 36.4 + - - -
31B CYS* 3.2 12.2 + - - -
308B ILE* 4.4 3.4 - - + +
311B LEU* 3.9 18.2 - - + +
312B GLN* 3.7 36.8 - - + +
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Residues in contact with LEU 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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9B LEU* 3.9 9.4 - - + -
14B PHE* 3.2 49.8 - - + -
24B PHE* 3.2 11.5 + - + +
27B ALA* 1.3 78.6 - - + +
29B GLU* 1.3 55.1 + - - +
31B CYS* 2.5 30.1 + - - +
32B GLY 2.9 8.0 + - - -
33B ALA* 3.3 14.6 + - + -
74B ILE* 4.0 15.3 - - + -
76B CYS* 3.2 26.5 - - - -
117B PHE* 4.3 14.8 - - + -
315B ALA* 3.8 22.9 - - + -
318B ILE* 5.9 1.6 - - + -
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Residues in contact with GLU 29 (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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7B LYS* 4.6 3.3 + - - -
14B PHE* 3.8 9.3 - - + -
25B ARG* 2.8 65.1 + - - +
26B LEU* 4.2 4.7 - - - +
27B ALA 3.2 0.6 - - - -
28B LEU* 1.3 78.5 - - - +
30B SER* 1.3 57.4 + - - +
31B CYS 3.0 0.2 - - - -
32B GLY* 3.0 15.8 + - - -
33B ALA 3.4 20.6 + - - +
34B GLU* 5.0 0.9 - - - -
35B CYS* 4.1 5.7 + - - +
53B PHE* 5.2 4.4 - - - -
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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