Contacts of the helix formed by residues 23 - 34 (chain B) in PDB entry 1SA4
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 LEU 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B GLU* 3.6 14.4 - - + +
22B PRO* 1.3 84.2 - - - +
24B TYR* 1.3 66.2 + - - +
26B LEU* 3.1 39.8 + - + +
27B ARG* 3.4 17.2 + - - +
62B TYR* 5.1 1.1 - - + -
68B VAL* 4.0 11.1 - - + +
69B PRO 5.4 1.1 - - - +
71B LEU* 4.0 22.4 - - + -
337B GLU* 3.6 20.0 - - - +
341B MET* 3.8 29.6 - - + -
387B LEU* 3.8 27.8 - - + -
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Residues in contact with TYR 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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350A THR* 2.7 32.7 + - - -
351A ILE* 3.3 37.4 + - + +
23B LEU* 1.3 70.1 - - - +
25B SER* 1.3 65.5 + - - +
26B LEU 3.1 1.0 + - - -
27B ARG* 3.2 55.1 + - - +
30B HIS* 3.8 29.6 - + - +
33B GLU* 5.5 2.5 - - + +
283B ARG 4.7 3.2 + - - -
286B GLY* 6.1 0.4 - - - -
331B HIS* 3.4 26.2 - + + -
333B GLN* 3.4 15.9 - - - +
334B ALA* 3.8 16.6 - - + -
337B GLU* 2.8 18.5 + - - +
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 1.3 76.5 - - - +
26B LEU* 1.3 67.1 + - - +
27B ARG 3.5 0.4 - - - +
30B HIS* 3.2 33.1 + - - +
56B GLN* 5.3 2.8 + - - +
59B PHE* 3.6 45.6 - - - +
284B PHE 4.8 0.7 + - - -
285B GLU 4.9 2.4 + - - -
286B GLY* 5.6 0.7 - - - -
334B ALA* 4.9 3.3 + - - +
337B GLU* 2.5 33.9 + - - +
341B MET* 4.3 1.3 - - - -
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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
----------------------------------------------------------
23B LEU* 3.1 26.8 + - + +
24B TYR 3.1 1.2 - - - -
25B SER* 1.3 93.9 - - - +
27B ARG* 1.3 65.8 + - - +
28B PRO* 3.7 2.8 - - - +
59B PHE* 3.9 21.3 - - + +
60B SER* 5.8 0.4 - - - -
62B TYR* 4.1 7.0 - - + +
63B LYS* 3.5 53.2 + - + +
68B VAL* 3.7 29.4 - - + -
341B MET* 4.1 13.7 - - + -
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Residues in contact with ARG 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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23B LEU 3.5 9.3 + - - +
24B TYR* 3.2 52.8 + - - +
25B SER 4.6 0.2 - - - +
26B LEU* 1.3 80.5 - - - +
28B PRO* 1.3 68.9 - - + +
29B GLU* 3.1 30.5 + - - +
30B HIS* 3.0 21.3 + - + +
31B ALA 4.2 0.9 + - - -
333B GLN* 4.7 11.1 + - - +
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Residues in contact with PRO 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU 3.7 3.3 - - - +
27B ARG* 1.3 82.8 - - + +
29B GLU* 1.3 79.7 + - + +
30B HIS 3.2 0.7 + - - -
31B ALA* 3.4 18.4 + - + +
32B ARG* 4.7 4.4 + - - -
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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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27B ARG* 3.1 28.3 + - - +
28B PRO* 1.3 99.9 - - + +
30B HIS* 1.3 62.8 + - - +
31B ALA 3.1 0.2 - - - -
32B ARG* 3.0 57.1 + - - +
33B GLU* 4.2 5.9 + - - +
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Residues in contact with HIS 30 (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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24B TYR* 3.8 38.2 - + - +
25B SER* 3.2 28.2 + - - +
27B ARG* 3.0 18.8 + - + +
29B GLU* 1.3 79.4 - - - +
31B ALA* 1.3 55.4 + - - +
33B GLU* 2.9 36.1 + - + +
56B GLN* 5.2 1.6 + - - +
59B PHE* 3.9 11.9 - + - -
283B ARG 3.4 14.4 + - - -
284B PHE* 2.8 56.6 + + - -
286B GLY* 6.1 0.2 - - - -
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Residues in contact with ALA 31 (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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27B ARG 4.2 0.8 + - - -
28B PRO 3.4 13.7 + - - +
29B GLU 3.1 0.6 - - - -
30B HIS* 1.3 78.4 - - - +
32B ARG* 1.3 61.2 + - + +
33B GLU 3.1 1.4 + - - -
34B ARG* 3.3 28.5 + - + +
56B GLN* 5.0 9.8 - - - +
284B PHE* 5.0 3.4 - - - -
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A GLU* 5.6 8.5 - - - +
28B PRO 5.0 3.0 + - - -
29B GLU* 3.0 50.4 + - - +
31B ALA* 1.3 79.2 - - + +
33B GLU* 1.3 65.5 + - - +
34B ARG 3.2 7.5 + - - +
36B GLN* 4.9 8.5 - - - +
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Residues in contact with GLU 33 (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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347A GLU 4.5 12.6 - - - +
348A LYS 5.1 2.5 - - - +
350A THR* 4.7 14.9 + - - +
351A ILE 5.8 0.7 + - - -
24B TYR* 5.5 2.0 - - - +
29B GLU 4.5 3.9 - - - +
30B HIS* 2.9 31.4 + - + +
32B ARG* 1.3 81.8 - - - +
34B ARG* 1.3 65.8 + - - +
35B LEU 3.7 0.7 + - - -
52B GLU* 4.7 1.0 - - - +
283B ARG* 3.0 82.5 + - + +
284B PHE* 3.6 13.3 - - + +
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 3.3 20.2 - - + +
32B ARG 3.2 6.7 - - - +
33B GLU* 1.3 82.8 - - - +
35B LEU* 1.3 67.9 + - - +
36B GLN* 3.5 10.7 + - - +
49B ALA* 4.6 3.0 + - - +
52B GLU* 3.3 29.0 + - - +
53B GLU* 3.3 39.4 + - - +
56B GLN* 3.9 26.6 - - - +
283B ARG* 5.5 1.1 - - - -
284B PHE* 3.3 30.7 - - + -
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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