Contacts of the strand formed by residues 36 - 46 (chain C) in PDB entry 1KPS
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 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ALA* 6.4 0.4 - - + -
13C ARG* 3.0 54.5 - - - +
28C PRO* 4.0 22.0 - - + +
29C THR 3.4 7.6 - - - +
30C LYS* 4.3 10.3 - - + +
31C ASN* 3.3 8.3 + - - -
34C GLY 5.6 0.2 - - - +
35C THR* 1.3 89.9 + - - +
37C ASN* 1.3 60.9 + - - +
38C LEU* 3.2 23.8 + - + +
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Residues in contact with ASN 37 (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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28C PRO* 4.0 3.1 - - - +
29C THR* 2.6 24.9 + - - +
30C LYS 5.1 0.4 - - - -
31C ASN* 3.3 29.7 + - - +
35C THR 3.9 0.2 + - - -
36C MET* 1.3 67.7 - - - +
38C LEU* 1.3 53.5 + - - +
39C MET* 2.7 38.4 + - - +
40C ASN* 2.8 40.4 + - - +
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Residues in contact with LEU 38 (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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6C LEU* 3.3 46.3 - - + +
9C LEU* 2.7 53.6 - - + +
10C ALA* 3.9 18.2 - - + +
13C ARG* 4.4 2.5 - - - -
28C PRO* 4.0 21.5 - - + -
36C MET* 3.2 28.3 + - + +
37C ASN* 1.3 71.2 + - - +
39C MET* 1.3 53.4 + - - +
41C TRP* 2.9 18.9 + - + +
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Residues in contact with MET 39 (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 ALA* 4.7 7.2 - - + -
6C LEU* 4.0 21.3 - - + -
9C LEU* 3.5 21.3 - - + -
37C ASN* 2.7 19.7 + - - +
38C LEU* 1.3 77.1 - - - +
40C ASN* 1.3 54.7 + - + -
62C MET 3.4 0.7 - - - +
63C LEU* 3.5 1.0 - - - -
64C PHE* 2.6 63.6 + - + +
65C LYS 3.0 34.5 - - - +
66C ASP* 3.9 15.3 - - - +
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Residues in contact with ASN 40 (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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29C THR* 2.7 58.0 + - - +
37C ASN* 2.8 34.0 + - - +
39C MET* 1.3 79.1 - - + +
41C TRP* 1.3 59.5 + - - +
61C ARG* 2.8 29.0 + - - +
62C MET 3.4 3.4 - - - -
63C LEU* 3.6 24.9 - - + +
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Residues in contact with TRP 41 (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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9C LEU* 3.5 24.2 - - + +
12C GLU* 4.0 2.7 - - + -
13C ARG* 3.4 31.6 - - + -
16C TRP* 5.1 4.3 - - + -
26C ALA* 3.6 38.4 - - + -
27C VAL 3.6 6.3 - - - +
28C PRO* 3.3 26.0 - - + +
29C THR* 3.9 0.2 - - - -
38C LEU* 2.9 30.8 + - + -
40C ASN* 1.3 89.9 - - - +
42C GLU* 1.3 60.4 + - - +
43C CYS* 4.1 6.3 - - - -
61C ARG* 3.5 3.8 - - - +
62C MET* 2.9 42.8 + - + +
64C PHE* 3.6 16.0 - + - -
109C ILE* 3.3 36.8 - - + -
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Residues in contact with GLU 42 (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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25C VAL* 4.4 2.8 - - - +
26C ALA* 3.7 0.9 + - - -
27C VAL* 3.0 40.0 + - + +
29C THR* 3.4 27.8 - - - +
41C TRP* 1.3 72.5 - - - +
43C CYS* 1.3 61.6 + - - +
60C LEU 4.0 2.9 - - - -
61C ARG* 3.2 38.8 + - - +
78C GLU* 4.8 0.9 - - - +
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Residues in contact with CYS 43 (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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25C VAL* 2.9 16.6 - - - +
26C ALA* 3.8 19.1 - - - -
41C TRP* 4.2 13.9 - - - -
42C GLU* 1.3 80.7 - - - +
44C ALA* 1.3 64.5 + - - +
59C LYS* 3.2 12.3 - - - +
60C LEU* 2.8 49.0 + - + +
62C MET* 4.0 29.4 - - - -
113C LEU* 4.1 5.4 - - + -
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Residues in contact with ALA 44 (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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23C GLY 4.9 2.2 - - - +
24C PHE* 3.3 7.4 - - - +
25C VAL* 2.8 52.4 + - + +
43C CYS* 1.3 80.2 - - - +
45C ILE* 1.3 67.3 + - - +
46C PRO* 4.3 1.1 - - - -
57C LEU* 5.2 11.7 - - + -
58C PHE 3.2 9.9 - - - +
59C LYS* 4.3 13.2 - - + -
60C LEU* 4.0 0.4 - - - +
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Residues in contact with ILE 45 (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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24C PHE* 3.7 26.5 - - + -
44C ALA* 1.3 79.6 - - - +
46C PRO* 1.3 72.1 - - - +
57C LEU* 4.6 1.1 - - - -
58C PHE* 2.6 50.7 + - + +
60C LEU* 3.9 13.9 - - + -
77C PHE* 5.6 3.1 - - + -
113C LEU* 3.2 48.0 - - + +
116C ILE* 4.0 17.9 - - + -
117C GLN* 3.9 16.6 - - + -
120C LEU* 4.7 8.3 - - + -
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Residues in contact with PRO 46 (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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22C PHE 4.0 1.6 - - - +
23C GLY* 3.5 31.2 - - - +
24C PHE* 3.2 35.2 - - + +
44C ALA 4.0 0.2 - - - +
45C ILE* 1.3 89.1 - - - +
47C GLY* 1.3 62.8 + - - +
55C GLY* 6.0 1.3 - - - +
56C GLY 3.3 9.2 - - - +
57C LEU* 3.9 13.2 - - + -
58C PHE* 4.7 0.4 - - - -
117C GLN* 2.7 33.3 + - - +
602C SO4 4.8 9.0 - - - +
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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