Contacts of the strand formed by residues 31 - 39 (chain M) in PDB entry 1KQ2
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 GLN 31 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23M THR* 4.1 14.9 - - + +
24M VAL 3.1 10.8 - - - +
25M PHE* 3.1 39.3 - - + -
26M PHE* 4.4 0.2 - - - -
29M GLY 4.8 5.1 + - - +
30M PHE* 1.3 99.1 - - + +
32M MET* 1.3 61.8 + - - +
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Residues in contact with MET 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B THR* 4.8 9.6 - - + +
64B THR* 6.0 0.2 - - - +
22M VAL 3.7 0.5 - - - +
23M THR* 3.2 4.9 - - - -
24M VAL* 2.6 42.0 + - + +
26M PHE* 3.7 29.2 - - + -
30M PHE* 3.5 28.7 - - + -
31M GLN* 1.3 75.2 - - - +
33M LYS* 1.3 60.6 + - - +
46M LEU* 4.1 18.4 - - + -
48M SER* 4.7 8.3 - - - +
49M GLN* 5.5 4.3 - - - +
53M HIS* 4.0 39.9 - - + +
55M ILE* 4.4 1.8 - - - -
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Residues in contact with LYS 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M GLU* 3.1 42.0 + - + +
22M VAL 3.2 9.2 - - - +
23M THR* 3.3 23.4 + - + +
32M MET* 1.3 76.0 - - - +
34M GLY* 1.3 54.0 + - - +
46M LEU* 4.2 2.7 - - - -
48M SER* 2.5 31.3 + - - -
49M GLN* 4.7 3.0 + - - +
66M GLU* 3.4 35.4 - - - +
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Residues in contact with GLY 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M GLU* 4.0 11.4 - - - -
22M VAL* 3.1 36.6 + - - +
33M LYS* 1.3 78.0 - - - +
35M VAL* 1.3 64.0 + - - -
46M LEU* 3.4 12.7 - - - +
47M ASN 3.2 13.5 - - - -
48M SER* 3.9 1.3 - - - -
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Residues in contact with VAL 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M PHE 4.9 0.4 - - - +
16M LYS 5.3 0.2 - - - +
19M GLN* 3.3 63.0 - - + +
20M THR 3.6 5.2 - - - +
21M GLU* 3.4 19.1 - - - +
34M GLY* 1.3 73.4 - - - -
36M ILE* 1.3 68.8 + - - +
37M GLU* 3.2 16.9 + - - +
46M LEU* 3.4 7.2 - - - -
47M ASN* 2.9 35.2 + - + +
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Residues in contact with ILE 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M LEU* 4.3 17.9 - - + +
15M PHE* 3.7 28.2 + - + -
16M LYS* 3.5 32.9 - - + +
20M THR 4.3 1.8 + - - -
22M VAL* 3.6 17.9 - - + -
24M VAL* 5.3 0.7 - - + -
35M VAL* 1.3 78.0 - - - +
37M GLU* 1.3 62.4 + - - +
38M GLU 3.8 21.1 - - - +
39M TYR* 4.7 6.3 - - + -
44M VAL* 4.0 20.9 - - + -
45M SER 3.8 1.8 - - - -
46M LEU* 3.5 22.9 - - + -
63M TYR* 5.0 10.1 - - + -
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Residues in contact with GLU 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M LYS* 3.4 18.2 - - - +
19M GLN* 4.0 18.7 + - - +
35M VAL* 3.2 14.8 + - - +
36M ILE* 1.3 74.2 - - - +
38M GLU* 1.3 74.2 + - + +
45M SER* 3.0 23.9 + - - +
47M ASN* 2.9 42.2 + - + +
52M GLN* 6.4 0.7 - - + -
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Residues in contact with GLU 38 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ILE* 2.8 46.6 - - + +
16M LYS* 4.4 16.2 - - - +
36M ILE* 3.6 7.2 - - - +
37M GLU* 1.3 91.9 - - - +
39M TYR* 1.3 69.1 + - - +
44M VAL* 3.7 0.5 - - - -
45M SER* 2.9 38.0 + - - +
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Residues in contact with TYR 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 3.7 13.6 - - - +
9M ASP* 3.6 37.4 + - - +
12M LEU* 3.7 50.7 - - + -
13M GLU* 3.1 29.8 + - - +
16M LYS* 4.3 15.7 + - + +
36M ILE* 4.7 3.6 - - + -
38M GLU* 1.3 82.4 - - - +
40M ASP* 1.3 80.0 + - - +
43M VAL* 3.7 13.5 - - - +
44M VAL* 4.2 14.4 - - + +
45M SER 4.7 0.2 - - - +
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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