Contacts of the strand formed by residues 38 - 45 (chain A) in PDB entry 1Q3L
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 MET 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.3 5.3 - - - -
35A ARG 2.9 32.4 + - - +
36A LYS* 3.8 13.0 - - + +
37A GLY* 1.3 84.5 - - - +
39A VAL* 1.3 68.1 + - - +
40A GLU* 3.5 10.6 + - + +
57A PRO* 4.8 17.5 - - + -
58A GLU* 6.3 2.0 - - + -
59A ASN* 5.1 12.6 - - + +
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Residues in contact with VAL 39 (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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32A ARG* 3.6 41.7 - - + +
33A ARG 3.4 8.5 - - - +
34A VAL* 4.2 11.7 - - + +
37A GLY 4.3 1.3 + - - +
38A MET* 1.3 72.9 - - - +
40A GLU* 1.3 60.3 + - - +
41A TYR* 4.0 25.4 - - + +
57A PRO* 3.6 3.6 - - - +
58A GLU* 2.8 51.6 + - - +
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Residues in contact with GLU 40 (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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32A ARG* 3.3 7.1 - - - +
33A ARG* 2.8 71.6 + - + +
35A ARG* 3.7 17.9 - - + +
38A MET* 4.0 12.4 - - + +
39A VAL* 1.3 78.3 - - - +
41A TYR* 1.3 62.3 + - - +
55A TRP* 3.5 18.7 - - + +
56A GLU 3.2 9.6 - - - +
57A PRO* 4.0 23.4 - - + +
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Residues in contact with TYR 41 (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 ILE* 3.6 20.9 - - + -
31A ASP 3.4 6.5 - - - +
32A ARG* 3.8 16.8 + - + -
39A VAL* 4.0 13.0 - - + +
40A GLU* 1.3 74.4 - - - +
42A TYR* 1.3 60.6 + - - +
43A LEU* 3.6 22.3 + - + +
54A THR 3.4 1.4 - - - +
55A TRP* 3.3 3.8 - - - -
56A GLU 2.9 30.9 + - - +
58A GLU* 3.8 33.8 + - + -
61A LEU* 3.8 18.8 - - + -
67A ILE* 3.5 32.2 - - + +
70A TYR* 4.3 10.1 - + + -
71A GLU* 2.7 30.2 + - + +
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Residues in contact with TYR 42 (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 ILE* 3.7 2.4 - - - -
30A ILE* 2.8 60.0 + - + +
31A ASP* 2.8 17.2 + - + +
41A TYR* 1.3 70.5 - - - +
43A LEU* 1.3 57.2 + - - +
50A GLU 4.7 1.6 + - - -
53A ASN* 3.4 49.2 + - + +
54A THR* 3.5 9.9 - - - -
55A TRP* 3.4 55.1 - + + -
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Residues in contact with LEU 43 (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 VAL* 4.1 11.7 - - + -
28A LYS 3.7 2.7 - - - +
29A ILE* 3.6 36.3 - - + -
30A ILE* 4.3 1.3 - - - -
41A TYR* 3.8 20.0 - - + +
42A TYR* 1.3 77.6 - - - +
44A LYS* 1.3 63.4 + - - +
45A TRP* 3.7 37.5 + - + -
53A ASN* 3.2 30.2 - - - +
54A THR 2.9 16.0 + - - +
56A GLU* 3.8 11.7 - - + -
61A LEU* 4.1 12.8 - - + -
7P ALA* 3.8 17.0 - - + -
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Residues in contact with LYS 44 (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 VAL* 3.9 4.2 - - - +
27A GLU* 2.8 64.6 + - + +
28A LYS* 3.0 32.9 + - + +
30A ILE* 3.9 11.8 - - + +
43A LEU* 1.3 72.2 - - - +
45A TRP* 1.3 67.5 + - - +
47A GLY* 4.3 2.4 - - - +
48A TYR 2.9 29.1 + - - +
49A PRO* 4.9 0.2 - - - -
50A GLU* 3.4 34.8 - - - +
53A ASN* 3.4 18.6 - - - +
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Residues in contact with TRP 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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24A TYR* 3.6 24.7 - - + -
25A ALA 3.7 13.7 - - - +
26A VAL* 3.7 8.5 - - + -
27A GLU* 4.1 0.4 - - - -
43A LEU* 3.7 19.2 + - + -
44A LYS* 1.3 93.3 + - - +
46A LYS* 1.3 65.8 + - - +
48A TYR* 3.1 30.0 + - + +
49A PRO 5.7 0.4 + - - -
52A GLU* 3.2 26.0 + - + -
53A ASN* 4.3 1.0 + - - -
54A THR* 3.0 31.2 + - - +
56A GLU* 3.7 15.5 - - + -
7P ALA* 3.6 46.9 - - + -
8P ARG 4.0 7.6 - - - -
9P MLZ 3.6 32.5 - - + -
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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