Contacts of the strand formed by residues 44 - 59 (chain A) in PDB entry 3SOQ
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 THR 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ARG* 3.2 5.2 - - - +
33A LEU* 2.8 56.9 + - - +
42A ASN 4.8 4.7 - - - +
43A ALA* 1.3 73.3 - - - +
45A ILE* 1.3 64.7 + - - +
46A VAL* 3.6 2.6 + - - +
401A FUC 4.7 7.2 + - - -
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Residues in contact with ILE 45 (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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30A ASP* 4.0 18.8 - - + +
31A LEU 3.6 5.4 - - - +
32A ARG* 4.0 28.9 - - - +
43A ALA 3.9 2.4 + - - +
44A THR* 1.3 75.8 - - - +
46A VAL* 1.3 60.4 + - - +
47A VAL* 3.4 31.0 - - - +
48A GLY* 3.9 6.1 - - - +
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Residues in contact with VAL 46 (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 LEU* 4.3 9.9 - - + -
31A LEU* 2.9 36.1 + - + +
32A ARG 4.3 1.6 - - - +
33A LEU* 3.8 44.4 - - + +
44A THR* 4.4 2.0 - - - +
45A ILE* 1.3 76.1 - - - +
47A VAL* 1.3 77.2 + - + +
65A ILE* 4.5 11.4 - - + -
78A THR* 5.5 0.3 - - - +
80A PHE* 6.0 0.9 - - + -
401A FUC 4.0 18.6 - - + +
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Residues in contact with VAL 47 (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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30A ASP* 3.0 6.8 - - - +
31A LEU* 2.8 43.3 + - + -
45A ILE* 3.4 5.5 - - - +
46A VAL* 1.3 97.3 - - + +
48A GLY* 1.3 62.7 + - - +
50A LEU* 3.8 16.6 - - + -
67A TRP* 4.0 9.9 - - + -
78A THR* 3.6 31.9 - - + +
87A GLN* 3.5 29.2 - - + +
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Residues in contact with GLY 48 (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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30A ASP* 3.8 10.8 - - - -
45A ILE* 3.9 8.1 - - - +
47A VAL* 1.3 75.4 - - - +
49A GLY* 1.3 61.0 + - - -
50A LEU* 3.4 4.2 - - - +
87A GLN* 3.1 24.5 + - - +
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Residues in contact with GLY 49 (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 ARG 3.4 6.0 + - - -
48A GLY* 1.3 73.0 - - - +
50A LEU* 1.3 65.9 + - - +
51A GLU* 5.3 2.0 - - - +
72A GLU* 4.9 4.9 - - - +
87A GLN* 4.9 3.5 + - - +
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Residues in contact with LEU 50 (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 ARG 3.5 12.3 - - - +
29A ARG* 3.0 31.0 + - - +
30A ASP* 3.8 20.2 - - - -
31A LEU* 3.9 13.5 - - + +
47A VAL* 3.8 11.4 - - + -
48A GLY 3.7 12.1 - - - +
49A GLY* 1.3 82.9 - - - +
51A GLU* 1.3 65.6 + - - +
53A ALA* 3.6 23.1 - - + -
67A TRP* 3.6 23.1 - - - +
69A ASP* 4.1 8.1 - - - +
72A GLU* 4.9 3.1 - - - +
76A LYS* 5.8 1.1 - - + +
87A GLN* 3.5 24.9 - - - +
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Residues in contact with GLU 51 (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 ARG 3.2 4.9 - - - +
29A ARG* 3.0 35.8 + - - +
49A GLY 5.3 2.2 - - - +
50A LEU* 1.3 76.1 - - - +
52A ASP* 1.3 68.0 + - - +
69A ASP* 3.1 17.8 + - - +
71A SER* 3.9 14.8 - - - -
72A GLU* 3.3 22.1 + - + +
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Residues in contact with ASP 52 (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 ARG* 2.9 41.1 + - - +
29A ARG* 3.9 5.3 + - - -
51A GLU* 1.3 85.5 - - - +
53A ALA* 1.3 66.8 + - - +
54A ALA* 3.2 3.0 + - - +
69A ASP* 3.1 10.9 + - - +
70A VAL* 3.1 37.5 + - + +
71A SER* 2.5 29.8 + - - +
43Z LYS* 6.5 0.2 - - - -
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Residues in contact with ALA 53 (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 ALA* 3.8 4.2 - - + +
28A ARG* 2.9 46.9 + - - +
30A ASP 4.4 0.4 - - - +
31A LEU* 4.0 13.9 - - + -
50A LEU* 3.6 27.4 - - + -
52A ASP* 1.3 69.8 - - - +
54A ALA* 1.3 60.0 + - - +
67A TRP* 3.9 8.3 - - + -
68A SER 3.2 11.4 - - - +
69A ASP* 3.8 4.2 + - - +
269A MET* 3.6 7.1 - - - +
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Residues in contact with ALA 54 (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 ALA* 3.3 4.2 - - - +
52A ASP 3.2 7.4 + - - +
53A ALA* 1.3 74.3 - - - +
55A ALA* 1.3 60.7 + - + +
68A SER* 2.9 16.8 + - - +
70A VAL* 4.2 10.3 - - + -
97A PRO 4.7 1.3 - - - +
98A ASP 5.0 1.3 - - - +
228A PHE* 4.6 1.9 - - - -
269A MET* 3.2 28.1 - - + +
270A ASP* 3.0 30.0 + - - +
42Z ILE* 4.0 19.5 - - + -
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Residues in contact with ALA 55 (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 ALA* 4.6 0.7 - - - +
54A ALA* 1.3 79.2 + - - +
56A VAL* 1.3 62.5 + - - +
67A TRP* 3.1 8.2 - - - +
68A SER* 2.9 37.8 + - - +
98A ASP 4.0 4.5 - - - +
99A GLY* 3.7 13.2 - - - -
100A LEU* 3.6 34.8 - - + +
270A ASP* 3.6 10.5 - - - +
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Residues in contact with VAL 56 (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 LEU* 3.9 36.3 - - + +
26A ALA* 4.0 14.8 - - + +
31A LEU* 4.0 24.7 - - + -
55A ALA* 1.3 76.6 - - - +
57A ASP* 1.3 66.1 + - - +
65A ILE* 4.2 0.4 - - + -
66A TYR 3.3 14.4 - - - +
67A TRP* 4.2 0.7 - - - +
100A LEU* 4.2 4.6 - - - +
270A ASP* 3.0 43.6 + - + +
271A ILE 4.2 1.1 - - - +
272A HIS* 2.8 27.1 + - + -
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Residues in contact with ASP 57 (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 LEU* 4.3 2.2 - - - +
56A VAL* 1.3 76.7 - - - +
58A PHE* 1.3 97.3 + - - +
65A ILE* 3.6 5.7 - - - +
66A TYR 2.8 29.4 + - - +
100A LEU* 3.6 20.1 - - + +
101A ALA* 3.2 10.0 - - - +
102A CYS* 2.8 36.7 + - - +
104A TRP* 6.0 0.3 - - - -
272A HIS* 3.5 28.6 + - - +
279A GLN* 4.3 3.4 + - - -
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Residues in contact with PHE 58 (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 LEU* 4.4 3.1 - - + -
57A ASP* 1.3 97.5 + - - +
59A VAL* 1.3 58.7 + - - +
60A PHE* 3.6 31.6 - + + -
64A LEU 3.2 16.2 - - - +
65A ILE* 4.1 4.5 - - + +
66A TYR 4.5 0.2 - - - +
80A PHE* 5.0 0.2 - - + -
102A CYS* 3.4 16.5 - - - +
272A HIS* 3.9 20.0 - + + -
273A ALA 3.6 25.4 - - - -
274A PHE* 3.9 24.9 - + + -
275A SER 3.7 21.5 - - - -
278A ARG* 4.6 3.6 - - + -
279A GLN* 2.8 49.0 + - + -
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Residues in contact with VAL 59 (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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58A PHE* 1.3 77.5 - - - +
60A PHE* 1.3 67.8 + - - +
61A SER* 4.1 4.7 - - - +
62A HIS* 3.0 50.6 + - + +
63A GLY 3.1 8.8 + - - -
64A LEU* 2.9 20.9 + - + -
66A TYR* 4.3 11.9 - - + -
102A CYS* 3.6 22.7 - - + -
104A TRP* 4.2 22.4 - - + -
124A LEU* 4.3 15.5 - - + -
279A GLN* 3.6 3.1 - - - -
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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