Contacts of the helix formed by residues 57 - 63 (chain C) in PDB entry 1KXT
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 PRO 57 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL* 3.5 15.9 - - + +
54C PRO* 3.4 13.9 - - + +
55C SER 3.5 1.0 - - - -
56C ARG* 1.3 94.7 - - - +
58C TRP* 1.3 64.5 + - - +
59C TRP* 3.5 50.7 - - + +
60C GLU* 3.2 17.7 - - + +
72C ARG* 4.6 1.8 + - - -
357C TRP* 3.3 32.1 - - + +
359C GLY 4.2 0.9 - - - +
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Residues in contact with TRP 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PHE* 3.7 22.4 - + + -
18C GLU* 3.0 25.7 - - - +
57C PRO* 1.3 66.7 - - - +
59C TRP* 1.3 102.5 + + + +
60C GLU* 2.9 11.2 + - - -
61C ARG* 3.2 22.5 + - - +
62C TYR* 4.2 12.7 - + - -
72C ARG* 5.4 0.4 - - - +
299C HIS* 3.6 32.5 - + - -
300C ASP* 4.9 13.5 - - - -
303C ARG* 3.7 20.0 - - - +
342C TYR* 3.6 18.2 - - - +
356C ASP 3.1 20.2 + - - -
357C TRP* 3.1 26.3 + - - -
358C ILE 3.4 10.8 - - - -
359C GLY* 3.8 5.4 - - - -
360C PRO* 4.6 0.4 - - - -
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Residues in contact with TRP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 3.8 22.2 - - + -
53C ASN 5.2 0.4 - - - -
54C PRO* 4.0 17.5 - - + -
57C PRO* 3.5 26.9 - - + -
58C TRP* 1.3 123.3 - + + +
60C GLU* 1.3 66.4 + - - +
61C ARG 3.1 2.0 - - - -
62C TYR* 3.4 21.3 + - + +
63C GLN* 3.8 26.2 - - - +
356C ASP 5.1 0.2 - - - -
357C TRP* 3.5 20.9 - - + +
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Residues in contact with GLU 60 (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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48C ASN* 3.0 31.0 + - - +
49C ILE 3.6 4.5 - - - +
50C VAL* 3.5 0.3 - - - -
51C VAL* 2.8 51.4 + - + +
56C ARG* 3.0 38.4 + - - -
57C PRO* 3.2 22.5 + - + +
58C TRP 2.9 1.8 + - - -
59C TRP* 1.3 81.9 - - - +
61C ARG* 1.3 65.8 + - + +
62C TYR 3.0 10.7 + - - -
63C GLN* 3.2 19.9 + - - +
72C ARG* 3.5 13.4 - - - +
114C THR* 4.2 0.3 - - - +
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Residues in contact with ARG 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 2.9 39.2 + - - +
21C TRP* 4.0 1.6 - - - -
43C SER* 3.7 22.4 + - - -
44C PRO* 2.8 57.3 + - + +
46C ASN* 5.3 1.7 + - - +
48C ASN* 3.8 22.0 + - - +
58C TRP* 3.6 11.9 - - - +
59C TRP 3.1 1.0 - - - -
60C GLU* 1.3 88.7 - - + +
62C TYR* 1.3 66.0 + - + +
63C GLN 3.3 3.3 + - - -
64C PRO* 5.2 1.9 - - - +
71C THR* 3.2 22.6 + - - -
72C ARG* 4.8 12.5 - - - +
73C SER* 2.8 35.9 + - - +
98C VAL* 4.3 2.1 - - - +
367C ILE* 6.1 0.4 - - - +
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Residues in contact with TYR 62 (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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15C HIS* 5.2 2.4 + - - -
17C PHE* 4.7 8.7 - + - -
43C SER* 5.2 1.0 - - - -
44C PRO* 3.8 17.5 - - + +
58C TRP* 4.2 25.8 - + - -
59C TRP* 3.4 24.0 + - + +
60C GLU 3.0 1.8 - - - -
61C ARG* 1.3 83.7 - - + +
63C GLN* 1.3 64.4 + - - +
64C PRO* 3.5 4.9 - - - -
96C ASP* 2.6 30.0 + - - -
98C VAL* 3.7 17.7 - - + -
101C HIS* 3.1 28.4 + - + -
165C LEU* 4.6 4.2 - - + +
195C ARG* 3.4 14.4 - - - -
197C ASP* 3.5 15.9 - - - -
299C HIS* 3.5 23.6 + + - -
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Residues in contact with GLN 63 (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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48C ASN* 3.2 4.4 - - - -
49C ILE* 2.6 67.8 + - + +
51C VAL* 4.5 4.4 - - - +
59C TRP* 3.8 34.0 + - - +
60C GLU 3.2 7.6 + - - +
61C ARG 3.3 0.6 - - - -
62C TYR* 1.3 84.2 - - - +
64C PRO* 1.3 63.9 - - - +
102C MET 4.3 0.2 - - - -
103C CYS* 3.6 9.9 - - - +
104C GLY* 2.6 24.9 + - - +
107C ALA* 5.1 0.2 - - - +
165C LEU* 4.5 14.7 - - + +
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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