Contacts of the strand formed by residues 18 - 31 (chain A) in PDB entry 3SY7
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 SER 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASP 4.7 2.0 + - - -
17A SER* 1.3 73.5 + - - +
19A LEU* 1.3 60.4 + - - +
20A ASP* 4.0 12.6 + - - -
49A THR 4.3 0.9 - - - -
50A TYR* 3.3 10.8 - - - -
51A GLU* 2.8 49.8 + - - -
420A LEU* 3.8 7.0 + - - -
421A GLY 3.5 17.5 + - - -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 1.3 74.3 - - - +
20A ASP* 1.3 62.8 + - - +
48A THR* 3.6 31.0 - - + -
49A THR 3.5 7.0 - - - +
50A TYR* 4.1 20.9 - - + -
418A SER 3.5 1.9 - - - -
419A ILE* 3.0 58.2 + - + -
420A LEU* 3.1 38.1 + - + +
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Residues in contact with ASP 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 4.0 12.6 + - - -
19A LEU* 1.3 86.4 + - - +
21A LEU* 1.3 60.5 + - - +
22A LEU* 4.1 0.7 - - + +
47A LEU 3.4 1.2 - - - +
48A THR* 3.2 7.1 - - - +
49A THR* 2.9 45.4 + - - +
417A LEU 3.7 17.5 - - - +
418A SER* 4.2 9.4 + - - +
419A ILE* 5.3 0.9 - - - -
420A LEU 4.7 2.4 - - - +
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASP* 1.3 74.7 - - - +
22A LEU* 1.3 63.4 + - - +
23A LEU* 4.3 17.5 - - + -
46A PHE* 4.1 15.7 - - + -
47A LEU 3.2 24.2 - - - +
48A THR* 3.7 17.5 - - + +
416A PRO* 4.8 0.4 - - - -
417A LEU* 2.8 56.4 + - + +
419A ILE* 4.6 20.7 - - + +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASP* 4.1 1.4 - - + +
21A LEU* 1.3 73.0 - - - +
23A LEU* 1.3 72.3 + - - +
24A ARG* 3.7 39.9 + - + +
45A GLY 3.7 0.9 - - - +
46A PHE* 3.5 5.2 - - - -
47A LEU* 2.7 54.2 + - + +
414A ASP* 3.9 15.3 - - + +
415A TYR 3.7 20.9 - - - -
416A PRO* 3.8 14.4 - - + -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.3 17.5 - - + -
22A LEU* 1.3 76.3 - - - +
24A ARG* 1.3 59.8 + - - +
25A ASN 4.2 0.7 - - - -
44A GLN* 4.1 10.3 - - - +
45A GLY 3.6 2.0 - - - +
46A PHE* 3.7 32.3 - - + -
413A VAL 3.5 1.3 - - - +
414A ASP* 3.2 5.0 - - - -
415A TYR* 2.7 59.4 + - + +
417A LEU* 4.0 15.9 - - + -
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 3.8 26.0 - - + +
23A LEU* 1.3 75.1 - - - +
25A ASN* 1.3 61.0 + - - +
26A TYR* 3.8 6.1 + - + -
43A THR 3.8 0.2 - - - +
44A GLN* 3.6 3.9 - - - +
45A GLY 2.7 44.2 + - - +
47A LEU* 4.6 10.0 - - + +
129A GLY 5.1 8.2 + - - -
131A ARG 3.5 11.9 + - - -
132A LEU* 3.1 49.4 + - + +
133A PHE* 5.2 0.4 - - - +
134A PRO* 5.2 3.6 - - - +
412A ILE* 3.7 18.9 - - + +
413A VAL 3.4 3.6 - - - -
414A ASP* 2.8 37.4 + - - +
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Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU 4.2 0.2 - - - -
24A ARG* 1.3 73.8 - - - +
26A TYR* 1.3 59.2 + - - +
27A TYR* 4.8 0.7 + - - +
42A TRP* 2.9 32.5 + - - +
43A THR 3.5 2.8 + - - -
44A GLN* 2.7 26.7 + - - +
73A LEU* 3.5 15.4 - - - +
411A LEU 3.6 1.9 - - - +
412A ILE* 3.4 4.3 - - - +
413A VAL* 2.8 46.6 + - + +
429A C8E 3.1 34.2 - - - +
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Residues in contact with TYR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 4.3 7.9 - - + -
25A ASN* 1.3 75.3 - - - +
27A TYR* 1.3 67.3 - - - +
28A PHE* 4.0 25.0 - + + -
41A ASP* 3.6 7.2 - - - +
42A TRP* 3.5 3.4 - - - -
43A THR* 2.7 44.1 + - - +
130A SER 4.6 1.3 + - - -
131A ARG* 3.9 13.9 + - - -
132A LEU* 3.8 54.3 - - + -
410A ARG* 3.5 34.4 + - + -
411A LEU 3.7 2.5 - - - -
412A ILE* 3.8 25.8 - - + +
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Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASN* 4.1 1.3 + - - +
26A TYR* 1.3 76.2 - - - +
28A PHE* 1.3 61.6 + - - +
29A ASN* 3.0 41.9 + - + -
40A VAL* 3.7 24.0 - - + +
41A ASP 3.6 0.7 - - - -
42A TRP* 3.9 30.3 - + + +
409A PHE* 3.9 26.9 - + - -
410A ARG* 3.3 6.9 - - - +
411A LEU* 2.8 49.4 + - + +
429A C8E 3.9 38.5 + - - -
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Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 4.0 16.4 - + + -
27A TYR* 1.3 76.4 - - - +
29A ASN* 1.3 61.7 + - - +
30A ARG* 3.4 42.4 - - + -
39A ARG* 3.3 46.2 - - - -
40A VAL* 3.4 3.5 - - - +
41A ASP* 2.7 50.4 + - + +
408A GLU* 3.7 13.5 - - + -
409A PHE 3.6 1.6 - - - -
410A ARG* 3.5 43.1 - - + -
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Residues in contact with ASN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A TYR* 3.0 34.5 + - + -
28A PHE* 1.3 76.4 - - - +
30A ARG* 1.3 66.5 + - - +
31A ASP* 4.3 2.3 + - - +
38A ASP* 3.4 20.4 + - - +
39A ARG 3.6 2.2 - - - -
40A VAL* 3.4 19.8 - - - +
407A ASN 4.0 0.5 - - - +
408A GLU* 3.5 1.6 - - - -
409A PHE* 2.7 49.2 + - + +
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.4 36.1 - - + -
29A ASN* 1.3 78.2 + - - +
31A ASP* 1.3 61.1 + - - +
38A ASP* 3.6 1.7 - - - -
39A ARG* 2.9 47.8 + - + +
292A ALA 5.7 1.0 + - - -
293A GLY* 3.7 27.5 + - - -
305A TYR* 4.0 10.4 + - - -
406A GLN* 3.3 40.9 - - - +
407A ASN 3.4 6.5 - - - +
408A GLU* 2.8 29.2 + - + +
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Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN* 4.5 2.1 + - - +
30A ARG* 1.3 75.0 - - - +
38A ASP* 3.8 36.5 + - - +
405A ASP 4.3 1.9 - - - +
406A GLN* 3.3 29.9 + - - +
407A ASN* 2.8 48.4 + - + +
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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