Contacts of the helix formed by residues 45 - 59 (chain C) in PDB entry 6XWQ
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 ILE 45 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 3.4 39.5 - - + -
41C VAL* 3.1 20.9 + - + +
44C TYR* 1.3 83.6 - - + +
46C LYS* 1.3 68.8 + - - +
47C PRO 3.2 2.5 - - - -
48C PHE* 2.8 35.9 + - + +
212C PHE* 4.4 14.4 - - + +
213C ALA* 3.6 31.5 - - + +
216C ALA* 5.4 1.3 - - + -
217C TYR* 5.8 1.1 - - + +
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Residues in contact with LYS 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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137B LEU* 6.1 0.4 - - - +
41C VAL 3.1 8.2 + - - +
42C LYS* 3.2 46.4 - - + +
45C ILE* 1.3 75.2 - - - +
47C PRO* 1.3 66.0 - - + +
49C GLY* 3.0 6.7 + - - +
50C ASP* 2.9 40.4 + - + +
213C ALA* 5.0 3.1 - - - -
214C LEU* 5.5 3.0 - - + +
217C TYR* 4.3 39.6 - - + +
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Residues in contact with PRO 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 4.5 22.9 - - + -
137B LEU* 3.4 35.2 - - + +
42C LYS 4.0 2.9 - - - +
43C THR 3.8 15.0 - - - +
44C TYR 3.3 22.0 - - - +
46C LYS* 1.3 97.8 - - + +
48C PHE* 1.3 61.1 + - + +
50C ASP* 4.2 2.0 - - + -
51C LEU* 2.9 27.5 + - - +
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Residues in contact with PHE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 6.4 1.1 - - + -
44C TYR 5.1 7.6 - - - -
45C ILE* 2.8 33.9 + - + +
47C PRO* 1.3 76.4 - - + +
49C GLY* 1.3 56.6 + - - +
51C LEU* 3.2 11.6 + - + +
52C PHE* 2.9 27.4 + - - +
206C TYR* 3.8 19.1 + - - +
209C ILE* 4.3 30.3 - - + +
210C GLY* 4.5 2.0 - - - -
213C ALA* 3.6 9.4 - - + -
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Residues in contact with GLY 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LYS* 3.0 7.2 + - - -
48C PHE* 1.3 79.7 - - - +
50C ASP* 1.3 56.7 + - - +
52C PHE* 3.2 3.6 + - - +
53C VAL* 2.9 33.3 + - - +
210C GLY 3.8 10.3 - - - -
213C ALA* 3.3 8.7 - - - +
214C LEU* 3.7 30.2 - - - +
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Residues in contact with ASP 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLN* 4.8 6.8 + - - +
137B LEU* 3.7 19.9 - - + +
46C LYS* 2.9 34.0 + - + +
47C PRO* 3.8 5.6 - - + +
49C GLY* 1.3 75.2 - - - +
51C LEU* 1.3 59.7 + - - +
53C VAL* 3.3 9.3 + - - +
54C ARG* 2.9 48.6 + - - +
214C LEU* 4.5 1.2 - - - +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 5.9 1.6 - - + +
137B LEU* 4.1 23.7 - - + +
140B VAL* 3.6 36.8 - - + -
47C PRO 2.9 17.8 + - - +
48C PHE* 3.4 10.1 - - + +
50C ASP* 1.3 76.4 - - - +
52C PHE* 1.3 56.4 + - - +
54C ARG* 3.3 4.1 + - - +
55C LEU* 2.9 44.1 + - + +
206C TYR* 3.3 26.9 - - + +
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Residues in contact with PHE 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PHE 2.9 12.7 + - - +
49C GLY* 3.2 7.2 + - - +
51C LEU* 1.3 78.0 - - - +
53C VAL* 1.3 58.8 + - + +
55C LEU* 3.2 6.4 + - + +
56C LEU* 3.0 47.0 + - + +
203C VAL* 3.8 22.4 - - + -
204C MET* 4.2 1.3 - - + -
206C TYR* 3.9 24.2 - + + -
207C ALA* 3.4 33.2 - - + -
210C GLY* 4.1 19.1 - - - -
211C VAL* 4.7 11.9 - - + -
214C LEU* 4.4 18.8 - - + -
277C THR* 3.3 29.8 - - - -
359C PRO* 5.4 1.3 - - + -
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLY 2.9 20.5 + - - +
50C ASP* 3.8 9.2 - - - +
52C PHE* 1.3 76.9 - - + +
54C ARG* 1.3 57.2 + - + +
56C LEU* 3.3 6.6 + - - +
57C LYS* 2.9 50.5 + - + +
214C LEU* 3.7 28.5 - - + -
278C ARG* 5.9 1.1 - - - +
359C PRO* 4.3 32.1 - - + +
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Residues in contact with ARG 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLN* 4.9 6.0 - - - +
137B LEU* 3.1 32.1 + - - -
138B ASN* 4.0 26.4 + - - +
140B VAL* 3.2 32.2 + - + +
141B PRO* 3.5 11.4 - - - +
142B THR* 2.9 34.6 + - - +
155B PRO* 6.1 0.4 - - - +
50C ASP* 2.9 37.1 + - - +
51C LEU* 3.6 2.0 - - - +
53C VAL* 1.3 77.5 - - + +
55C LEU* 1.3 55.7 + - - +
57C LYS* 3.3 18.2 + - - +
58C MET 2.9 22.9 + - - -
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL* 3.8 28.0 - - + -
158B PHE* 4.1 9.2 - - + -
51C LEU* 2.9 28.5 + - + +
52C PHE* 3.2 7.4 + - - +
54C ARG* 1.3 76.8 - - - +
56C LEU* 1.3 58.4 + - - +
58C MET* 2.9 42.6 + - + +
59C LEU* 3.0 17.3 + - - +
203C VAL* 4.2 28.7 - - + -
206C TYR* 4.3 28.5 - - + -
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Residues in contact with LEU 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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52C PHE* 3.0 50.8 + - + +
53C VAL 3.9 3.6 - - - +
55C LEU* 1.3 75.7 - - - +
57C LYS* 1.3 60.3 + - - +
59C LEU* 3.9 23.3 + - + +
60C VAL* 4.2 0.7 - - - +
200C VAL* 5.5 1.1 - - + -
203C VAL* 3.7 22.0 - - + -
204C MET* 4.0 4.7 - - + -
277C THR* 3.5 4.5 - - - +
279C SER* 3.1 31.2 - - - +
281C SER 5.6 2.1 - - - +
282C GLY* 3.9 23.6 - - - -
357C GLY 4.6 3.1 - - - +
358C VAL* 3.5 13.8 - - - +
359C PRO* 4.1 15.0 - - + -
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Residues in contact with LYS 57 (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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142B THR* 2.8 43.3 + - + +
143B ASN* 4.6 2.3 - - - +
53C VAL* 2.9 41.6 + - + +
54C ARG* 3.6 14.9 - - - +
55C LEU 3.1 0.2 - - - -
56C LEU* 1.3 76.1 - - - +
58C MET* 1.3 63.2 + - - +
59C LEU 3.2 1.3 - - - -
60C VAL* 3.2 19.9 - - + +
61C MET 4.7 0.2 + - - -
358C VAL* 3.6 36.1 - - + -
359C PRO 5.6 0.7 - - - +
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Residues in contact with MET 58 (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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141B PRO* 3.1 44.6 - - + +
142B THR 3.2 9.3 + - - -
144B PRO* 3.6 13.7 - - + +
158B PHE* 4.3 13.7 - - + -
159B PHE* 4.0 19.5 - - + -
162B ILE* 4.9 5.6 - - + -
54C ARG 2.9 7.6 + - - +
55C LEU* 2.9 36.4 + - + +
57C LYS* 1.3 76.8 - - - +
59C LEU* 1.3 82.6 + - + +
60C VAL 3.3 4.2 + - - -
61C MET 4.4 0.2 + - - -
62C PRO* 3.4 20.3 - - - +
199C ILE* 4.6 8.1 - - + -
203C VAL* 5.1 1.3 - - + -
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Residues in contact with LEU 59 (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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159B PHE* 5.6 0.7 - - + -
55C LEU 3.0 13.7 + - - +
56C LEU* 3.9 14.7 + - + +
57C LYS 3.2 0.8 - - - -
58C MET* 1.3 94.2 - - + +
60C VAL* 1.3 57.0 + - - -
62C PRO* 4.7 2.2 - - - -
63C ILE* 3.1 30.1 - - + +
196C MET* 4.0 22.2 - - + -
199C ILE* 3.6 26.5 - - + -
200C VAL* 3.6 24.0 - - + -
203C VAL* 3.6 35.0 - - + -
281C SER* 3.3 11.9 + - - +
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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
------------------------------------------------------------
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