Contacts of the helix formed by residues 10 - 23 (chain C) in PDB entry 4WCX
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 ASN 10 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A ARG* 3.5 26.2 + - - +
386A MET* 3.4 15.9 - - - +
465A TYR* 2.9 27.6 + - - -
7C ASP 4.3 8.0 + - - +
8C PHE 3.8 2.2 + - - -
9C ILE* 1.3 72.6 - - - +
11C ASP* 1.3 59.7 + - - +
12C GLU* 3.1 8.3 + - - +
13C LYS* 2.9 43.2 + - + +
14C ILE* 3.0 34.6 + - - +
251C TYR* 6.1 0.4 - - - -
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Residues in contact with ASP 11 (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 ILE* 4.0 3.4 + - - +
10C ASN* 1.3 73.8 + - - +
12C GLU* 1.3 59.3 + - - +
14C ILE* 3.3 1.6 + - - +
15C ARG* 2.8 33.1 + - - +
197C HIS* 4.5 7.4 + - - -
244C TYR* 2.6 42.0 + - - +
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Residues in contact with GLU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A MET* 3.9 9.4 - - + -
453A ARG* 3.2 27.6 + - - -
465A TYR* 3.4 36.7 + - + +
466A PHE* 4.1 4.3 - - - -
10C ASN* 3.1 9.9 + - - +
11C ASP* 1.3 80.0 + - - +
13C LYS* 1.3 57.4 + - - +
15C ARG* 3.4 7.3 + - - +
16C GLN* 2.8 67.9 + - - +
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Residues in contact with LYS 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ARG 4.7 1.0 + - - -
386A MET* 3.5 25.6 - - + +
387A GLY* 3.1 41.7 - - - +
388A ARG* 6.3 0.2 - - + -
7C ASP 5.8 0.2 + - - -
8C PHE* 4.6 12.2 + - - +
10C ASN* 2.9 31.8 + - - +
12C GLU* 1.3 75.2 - - - +
14C ILE* 1.3 63.4 + - - +
16C GLN* 3.3 3.5 + - - +
17C ASP* 3.0 26.5 + - - +
251C TYR* 3.4 48.6 - - + +
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Residues in contact with ILE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 3.8 28.5 - - + -
10C ASN 3.0 20.2 + - - +
11C ASP 3.9 3.4 - - - +
13C LYS* 1.3 76.0 - - + +
15C ARG* 1.3 63.3 + - - +
17C ASP* 3.1 9.4 + - - +
18C LEU* 2.9 27.5 + - + +
244C TYR* 3.6 44.2 - - + +
247C VAL* 4.2 14.1 - - + -
248C ALA* 3.9 18.2 - - + -
251C TYR* 4.0 23.3 - - + -
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Residues in contact with ARG 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP* 2.8 24.0 + - - +
12C GLU* 3.8 10.3 - - - +
14C ILE* 1.3 78.3 - - - +
16C GLN* 1.3 56.8 + - + +
18C LEU* 3.2 36.3 + - - +
19C GLU* 2.9 52.5 + - + +
22C LYS* 4.8 6.7 - - - +
240C TYR* 4.0 19.0 + - - -
241C ASP* 5.1 4.2 + - - +
244C TYR* 4.1 13.7 - - + -
505C NA 4.3 5.5 - - - -
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Residues in contact with GLN 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A MET* 3.6 11.4 - - - +
388A ARG* 4.3 0.7 + - - -
405A PHE* 3.5 24.5 - - - -
466A PHE* 2.9 33.3 + - - +
12C GLU* 2.8 47.5 + - - +
13C LYS* 3.6 4.9 - - - +
15C ARG* 1.3 75.4 - - + +
17C ASP* 1.3 66.0 + - - +
19C GLU* 3.3 6.2 + - - +
20C LYS* 2.9 34.3 + - + +
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Residues in contact with ASP 17 (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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13C LYS* 3.0 18.8 + - - +
14C ILE* 3.1 8.2 + - - +
16C GLN* 1.3 79.7 - - - +
18C LEU* 1.3 57.4 + - - +
20C LYS* 3.5 6.1 + - - +
21C ALA* 3.0 27.7 + - - +
45C GLU* 3.5 35.4 - - - +
48C ALA* 3.7 18.3 - - + +
49C VAL* 5.9 0.2 - - - +
247C VAL* 3.8 8.5 - - + +
251C TYR* 2.6 40.7 + - - -
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 2.9 20.5 + - + +
15C ARG* 3.5 43.3 - - - +
17C ASP* 1.3 75.2 - - - +
19C GLU* 1.3 66.0 + - - +
21C ALA* 3.3 14.1 + - + +
22C LYS* 3.3 20.8 + - - +
48C ALA* 4.3 7.9 - - + +
52C ASN* 5.1 0.9 - - - +
241C ASP* 4.2 5.2 - - - +
243C LYS* 4.0 26.5 - - + -
244C TYR* 4.1 28.5 - - + +
247C VAL* 4.2 21.5 - - + -
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ARG* 2.9 42.0 + - + +
16C GLN* 3.3 6.7 + - - +
18C LEU* 1.3 75.0 - - - +
20C LYS* 1.3 65.1 + - + +
22C LYS* 3.0 40.7 + - - +
23C LYS* 3.7 13.6 + - - +
506C NA 2.3 30.8 - - - -
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Residues in contact with LYS 20 (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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401A GLN* 6.0 5.9 - - - +
405A PHE* 6.3 2.5 - - + -
16C GLN* 2.9 23.5 + - + +
17C ASP* 3.8 5.2 - - - +
19C GLU* 1.3 76.5 - - + +
21C ALA* 1.3 62.8 + - - +
23C LYS* 3.0 27.2 + - - +
24C ALA* 3.2 11.7 + - - +
45C GLU* 3.0 32.0 + - + +
49C VAL* 5.4 1.8 - - + -
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Residues in contact with ALA 21 (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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17C ASP 3.0 12.7 + - - +
18C LEU* 3.4 12.6 - - + +
19C GLU 3.2 0.4 - - - -
20C LYS* 1.3 76.3 - - - +
22C LYS* 1.3 61.3 + - - +
23C LYS 3.3 0.3 + - - -
24C ALA* 3.3 14.8 + - - +
48C ALA* 3.2 39.0 - - + +
49C VAL* 3.6 15.8 - - - +
52C ASN* 3.8 17.7 + - + +
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Residues in contact with LYS 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ARG* 4.8 8.3 - - - +
18C LEU* 3.6 12.4 + - - +
19C GLU* 3.0 42.3 + - - +
20C LYS 3.1 0.8 - - - -
21C ALA* 1.3 78.5 - - - +
23C LYS* 1.3 63.3 + - + +
24C ALA 3.7 3.1 + - - +
52C ASN* 3.8 26.1 + - - +
506C NA 3.4 11.6 - - - -
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Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLU 3.7 16.2 - - - +
20C LYS* 3.0 17.7 + - - +
22C LYS* 1.3 80.3 - - + +
24C ALA* 1.3 65.1 + - - +
25C THR* 3.6 7.3 + - - +
28C ASP* 4.9 0.3 - - - +
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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