Contacts of the strand formed by residues 54 - 63 (chain B) in PDB entry 1SPS
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 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B LEU 5.2 2.2 - - - +
20B LEU* 3.7 47.6 - - + +
21B ASN 4.8 5.2 - - - +
22B PRO* 5.2 15.0 - - + +
24B ASN* 5.3 8.1 - - + +
46B SER* 5.3 6.5 - - - -
47B ASP 3.8 10.8 - - - +
48B PHE* 3.4 25.9 - - + -
52B LYS 4.0 4.3 - - - +
53B GLY* 1.3 68.4 - - - +
55B ASN* 1.3 59.9 + - - +
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Residues in contact with ASN 55 (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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20B LEU* 4.1 4.6 - - - +
46B SER* 3.5 2.9 - - - -
47B ASP* 2.8 45.6 + - - +
48B PHE 3.9 0.2 - - - +
49B ASP* 3.7 29.1 + - - +
52B LYS* 4.4 11.0 - - + +
53B GLY 3.0 22.1 + - - +
54B LEU* 1.3 74.6 - - - +
56B VAL* 1.3 64.1 + - - +
57B LYS* 3.2 33.5 + - - +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 3.7 29.7 + - + +
19B LEU* 4.0 24.2 - - + -
20B LEU* 3.8 24.4 - - + +
44B SER* 4.2 10.5 - - - -
45B VAL 3.3 10.5 - - - +
46B SER* 4.8 2.2 - - - -
55B ASN* 1.3 81.1 - - - +
57B LYS* 1.3 63.4 + - - +
58B HIS* 3.5 37.4 + - + +
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Residues in contact with LYS 57 (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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43B LEU 3.6 1.6 - - - +
44B SER* 3.3 2.4 - - - -
45B VAL* 2.7 40.1 + - - +
47B ASP* 3.3 35.0 - - + -
49B ASP* 5.7 2.0 + - - -
55B ASN* 3.2 23.0 + - - +
56B VAL* 1.3 72.9 + - - +
58B HIS* 1.3 61.0 + - - +
59B TYR* 3.7 24.7 - - + +
95B CYS* 3.8 15.5 - - - -
1E GLU* 3.7 36.7 + - + +
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Residues in contact with HIS 58 (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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12B ARG* 3.4 41.0 - - - +
15B SER* 3.3 24.9 - - - -
16B GLU* 3.4 18.2 + - + -
32B ARG* 3.5 9.0 + - - -
42B CYS* 3.7 10.3 - - - -
43B LEU 3.3 4.9 - - - -
44B SER* 2.7 23.1 + - - -
56B VAL* 3.5 27.1 - - + +
57B LYS* 1.3 72.0 - - - +
59B TYR* 1.3 60.6 + - - +
-1E GLN 4.4 7.9 + - - +
0E PTR 3.1 16.0 - - + +
1E GLU* 2.9 26.7 + - - +
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Residues in contact with TYR 59 (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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42B CYS* 3.2 3.3 - - - -
43B LEU* 2.8 44.8 + - + +
45B VAL* 3.5 32.8 - - + -
57B LYS* 3.7 16.5 - - + +
58B HIS* 1.3 75.7 - - - +
60B LYS* 1.3 60.9 + - - +
61B ILE 3.5 0.5 + - - -
71B ILE* 4.0 21.8 - - + -
93B GLY 4.9 1.0 + - - -
94B LEU* 3.9 17.4 - - + -
95B CYS* 3.0 35.7 + - - +
0E PTR 3.9 2.5 - - - -
1E GLU* 3.5 34.9 + - + +
2E GLU 4.2 3.8 - - - -
3E ILE* 4.0 26.9 - - + -
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Residues in contact with LYS 60 (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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34B SER* 3.2 18.4 + - - -
36B THR* 4.0 7.8 - - - -
37B THR* 3.1 27.7 + - + +
40B ALA* 4.1 10.5 - - + -
41B TYR 3.6 14.1 - - - +
59B TYR* 1.3 71.0 - - - +
61B ILE* 1.3 58.2 + - - +
62B ARG* 3.5 50.4 + - + +
71B ILE* 3.9 21.5 - - - +
0E PTR 3.4 46.3 + - + +
1E GLU 4.6 3.2 + - - -
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Residues in contact with ILE 61 (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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31B VAL* 4.0 23.3 - - + -
40B ALA* 3.9 0.2 - - - -
41B TYR* 3.0 33.9 + - + +
42B CYS 4.3 1.1 - - - -
43B LEU* 3.8 28.5 - - + +
60B LYS* 1.3 70.7 - - - +
62B ARG* 1.3 61.0 + - - +
63B LYS 3.6 1.6 + - - -
69B PHE* 3.9 17.3 - - + -
70B TYR 3.6 6.5 - - - +
71B ILE* 3.9 15.3 - - + -
80B LEU* 3.9 19.3 - - + -
83B LEU* 3.8 40.8 - - + -
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Residues in contact with ARG 62 (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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37B THR* 5.6 5.1 + - + +
40B ALA* 4.7 7.0 - - + -
60B LYS* 3.5 46.6 + - + +
61B ILE* 1.3 71.8 - - - +
63B LYS* 1.3 61.3 + - - +
64B LEU 3.5 0.6 + - - -
69B PHE* 3.6 3.0 - - - -
70B TYR* 3.0 68.0 + - + +
71B ILE 5.5 3.1 - - - -
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Residues in contact with LYS 63 (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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39B GLY* 3.5 33.1 + - - +
40B ALA* 4.8 2.4 - - - +
41B TYR* 5.2 4.0 + - + -
61B ILE 3.6 1.6 + - - -
62B ARG* 1.3 71.5 - - - +
64B LEU* 1.3 74.5 + - - +
65B ASP* 3.8 2.1 + - - +
66B SER 5.8 1.6 - - - -
67B GLY* 4.8 10.5 - - - +
69B PHE* 3.5 35.9 - - + -
70B TYR* 4.7 0.7 - - - -
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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