Contacts of the strand formed by residues 25 - 33 (chain L) in PDB entry 3MQT
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 ASN 25 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59I GLU* 2.9 37.2 + - - +
15L VAL 3.1 15.7 - - - +
16L ASN* 3.9 19.8 + - - +
23L SER* 3.1 21.8 + - - +
24L GLU* 1.3 75.0 - - - +
26L THR* 1.3 63.5 + - - +
45L GLY 4.6 2.4 - - - +
47L PRO* 3.7 20.7 - - + +
312L LYS* 3.2 21.0 + - - +
345L LEU* 3.7 9.6 - - - +
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Residues in contact with THR 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L VAL* 2.9 49.7 + - + +
25L ASN* 1.3 77.7 - - - +
27L VAL* 1.3 70.6 + - - +
28L ILE* 4.0 6.3 - - + -
42L GLU* 2.6 35.5 + - - +
43L ALA 4.3 0.5 + - - -
45L GLY 5.5 0.9 - - - -
47L PRO* 3.8 5.7 - - - +
312L LYS* 3.9 14.9 + - - +
313L THR* 4.1 6.1 - - - +
345L LEU* 3.9 12.3 - - + -
349L LEU* 4.0 16.6 - - + -
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Residues in contact with VAL 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L PHE* 3.8 39.0 - - + -
13L ILE 3.7 7.4 - - - +
14L PRO* 4.7 2.0 - - + -
26L THR* 1.3 77.7 + - - +
28L ILE* 1.3 64.2 + - - +
29L VAL* 4.4 0.7 - - + -
42L GLU* 3.2 6.4 - - - +
43L ALA* 3.0 45.0 + - + +
45L GLY 4.4 2.9 - - - +
47L PRO* 3.4 40.8 - - + +
50L MET* 3.8 15.9 - - + -
51L LYS 5.6 0.2 - - - +
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Residues in contact with ILE 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L GLU 3.4 2.4 - - - +
12L PHE* 3.6 1.6 - - - -
13L ILE* 2.8 54.1 + - + +
15L VAL* 3.8 25.8 - - + -
26L THR* 4.2 7.2 - - + -
27L VAL* 1.3 72.3 - - - +
29L VAL* 1.3 63.3 + - - +
40L LEU* 4.1 25.8 - - + -
41L GLY 3.6 8.3 - - - +
42L GLU* 4.5 1.1 - - - -
315L ILE* 4.1 18.6 - - + -
349L LEU* 4.1 15.3 - - + -
373L LEU* 4.4 6.7 - - + -
378L VAL* 3.9 28.9 - - + -
386L PHE* 5.6 1.3 - - + -
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Residues in contact with VAL 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L VAL* 4.4 2.7 - - + -
11L GLU 3.3 4.0 - - - +
12L PHE* 3.9 33.2 - - + -
27L VAL* 4.2 1.8 - - + +
28L ILE* 1.3 76.2 - - - +
30L LYS* 1.3 62.4 + - - +
31L VAL* 4.3 6.7 - - + -
39L GLY 3.7 0.7 - - - +
40L LEU* 3.4 8.0 - - - +
41L GLY 2.7 37.4 + - - +
43L ALA* 4.2 11.2 - - + +
104L GLY* 3.8 26.7 - - - +
105L ILE* 3.8 33.2 - - + -
108L ALA* 3.8 6.3 - - + +
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Residues in contact with LYS 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L SER* 3.8 1.6 + - - +
10L VAL* 3.5 2.4 - - - -
11L GLU* 2.8 60.0 + - + +
13L ILE* 4.2 15.0 - - + -
28L ILE 3.9 0.4 + - - -
29L VAL* 1.3 74.9 - - - +
31L VAL* 1.3 61.9 + - - +
32L THR* 4.0 11.8 + - - +
38L TYR* 3.7 32.8 - - + -
39L GLY 3.5 2.2 - - - -
40L LEU* 3.9 16.4 - - + -
386L PHE* 3.4 60.8 + - + -
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Residues in contact with VAL 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ILE* 3.7 31.0 - - + -
9L SER 3.5 4.5 - - - +
10L VAL* 4.4 13.0 - - + -
29L VAL* 4.3 9.6 - - + -
30L LYS* 1.3 73.1 - - - +
32L THR* 1.3 63.7 + - - +
38L TYR* 3.1 3.2 - - - -
39L GLY 2.8 35.5 + - - +
105L ILE* 4.4 6.7 - - + -
108L ALA* 3.4 28.0 - - + -
109L LEU* 3.9 15.9 - - + -
112L LEU* 3.7 23.3 - - + +
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Residues in contact with THR 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ILE* 3.6 3.0 - - - -
8L VAL* 2.6 35.6 + - + -
9L SER* 3.1 30.2 + - - +
11L GLU* 4.6 2.8 + - - -
30L LYS* 4.0 16.7 + - - +
31L VAL* 1.3 74.9 - - - +
33L ASP* 1.3 66.2 + - - +
36L GLY* 3.8 19.1 - - - +
37L VAL 3.3 11.7 - - - +
38L TYR* 3.7 10.7 - - + +
112L LEU* 4.7 1.8 - - - -
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Residues in contact with ASP 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L ALA* 4.0 5.6 - - - +
6L ASN 3.2 17.3 - - - +
7L ILE* 4.0 0.7 - - - +
8L VAL* 3.9 9.2 - - - +
31L VAL 4.3 0.2 + - - -
32L THR* 1.3 80.3 - - - +
34L GLU* 1.3 60.4 + - - +
35L ASN* 2.9 18.6 + - - +
36L GLY* 3.0 14.7 + - - -
37L VAL* 2.9 41.6 + - - +
112L LEU* 3.9 8.6 - - + +
116L GLN* 2.7 42.3 + - - +
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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