Contacts of the strand formed by residues 49 - 56 (chain C) in PDB entry 1KI1
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 GLU 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C MET* 3.7 3.8 - - - -
46C ILE 2.8 28.9 + - - +
47C GLY 3.3 3.1 - - - +
48C GLY* 1.3 85.5 - - - +
50C PRO* 1.3 75.5 - - - +
51C TYR* 3.0 39.3 + - + +
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Residues in contact with PRO 50 (chain C).
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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1C MET* 3.6 30.5 - - + +
43C THR* 5.4 6.7 - - - -
44C VAL 3.4 7.9 - - - +
45C MET* 3.7 21.3 - - + -
48C GLY 4.0 2.7 - - - +
49C GLU* 1.3 99.0 - - + +
51C TYR* 1.3 65.6 + - - +
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Residues in contact with TYR 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.8 5.4 - - + -
2C GLN* 4.7 12.1 - - + -
4C ILE* 4.5 8.7 - - + -
42C VAL 3.7 0.5 - - - +
43C THR* 3.1 4.0 - - - -
44C VAL* 2.7 43.9 + - - +
46C ILE* 3.8 24.4 + - + +
49C GLU* 3.0 54.6 - - + +
50C PRO* 1.3 76.3 - - - +
52C THR* 1.3 63.5 + - - +
173C ILE* 4.1 23.6 - - + -
177C LEU* 3.6 45.5 - - + +
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Residues in contact with THR 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.2 30.3 + - - +
2C GLN 3.7 13.1 + - - +
3C THR* 3.4 19.8 - - - +
4C ILE* 2.8 36.5 + - - +
41C ALA* 4.5 13.5 - - + -
42C VAL 3.6 8.7 - - - +
43C THR* 3.4 14.3 - - + +
51C TYR* 1.3 75.0 - - - +
53C LEU* 1.3 63.3 + - - +
1368D GLY* 5.6 2.5 - - - +
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Residues in contact with LEU 53 (chain C).
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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3C THR* 4.8 0.2 - - - -
4C ILE* 3.7 13.9 - - + +
6C CYS* 3.8 31.4 - - + -
23C TYR* 4.1 22.0 - - + +
40C TYR 3.4 1.7 - - - +
41C ALA* 3.1 6.1 - - - +
42C VAL* 2.8 50.2 + - + +
44C VAL* 4.3 3.6 - - + -
51C TYR 4.0 0.4 + - - -
52C THR* 1.3 74.2 - - - +
54C GLY* 1.3 58.8 + - - +
55C LEU* 3.9 9.0 - - + -
169C PHE* 4.1 22.4 - - + +
172C ALA* 5.3 2.7 - - + -
173C ILE* 3.6 40.6 - - + -
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Residues in contact with GLY 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C THR* 4.5 7.7 + - - -
4C ILE 2.8 16.1 + - - -
5C LYS* 3.8 0.8 - - - -
6C CYS* 2.9 30.0 + - - +
40C TYR 3.5 5.2 - - - -
41C ALA* 4.4 3.1 - - - -
53C LEU* 1.3 72.9 - - - +
55C LEU* 1.3 61.1 + - - -
56C PHE* 3.6 13.7 - - - -
1369D MET* 4.5 11.9 - - - -
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Residues in contact with LEU 55 (chain C).
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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6C CYS* 3.7 16.4 - - - +
8C VAL* 5.6 0.4 - - + -
20C LEU* 4.2 11.9 - - + -
23C TYR* 4.1 14.8 - - + -
24C THR* 3.6 30.5 - - + -
37C PHE* 3.6 19.0 - - + -
39C ASN* 3.3 9.2 - - - +
40C TYR* 2.7 36.4 + - + +
42C VAL* 4.1 12.8 - - + -
53C LEU* 4.2 18.2 - - + -
54C GLY* 1.3 69.8 - - - -
56C PHE* 1.3 63.8 + - - +
169C PHE* 3.6 30.1 - - + -
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Residues in contact with PHE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LYS* 3.9 37.2 - - + -
6C CYS 3.1 12.8 + - - +
7C VAL* 3.8 14.0 - - + +
8C VAL* 3.0 29.8 + - - +
20C LEU* 4.4 3.8 - - - +
37C PHE* 4.8 0.2 - - - -
39C ASN* 3.2 36.1 - - - +
54C GLY* 3.6 18.2 - - - -
55C LEU* 1.3 77.4 - - - +
57C ASP* 1.3 61.7 - - - +
71C SER* 5.5 4.3 - - - -
1369D MET* 3.5 29.2 - - + -
1370D PRO* 5.9 0.7 - - + -
1373D SER* 3.7 15.0 - - - -
1376D LEU* 3.9 25.1 - - + -
1380D GLN* 4.4 1.8 - - - +
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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