Contacts of the helix formed by residues 10 - 23 (chain C) in PDB entry 4Y1L
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 10 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B ARG* 2.4 37.5 + - - -
9C ALA* 1.3 70.7 - - - +
11C PRO* 1.4 81.9 - - + +
13C GLN* 3.3 20.8 - - - +
14C GLU* 2.9 25.6 + - + +
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Residues in contact with PRO 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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17B ARG* 3.7 25.8 + - - +
9C ALA* 3.6 10.1 - - + -
10C GLU* 1.4 105.6 - - + +
12C VAL* 1.3 59.0 + - + +
14C GLU* 3.4 3.3 + - - +
15C GLU* 2.9 27.7 + - - +
69C PRO* 5.4 4.9 - - + -
105C PRO* 3.9 22.5 - - + +
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Residues in contact with VAL 12 (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 ALA* 3.1 24.8 + - + +
11C PRO* 1.3 75.7 - - + +
13C GLN* 1.3 61.3 + - - +
15C GLU* 3.1 9.4 + - - +
16C LEU* 2.9 36.2 + - + +
40C THR* 6.0 1.1 - - - +
64C LEU* 4.1 28.3 - - + -
68C TYR* 3.6 31.4 - - + +
69C PRO* 4.0 13.2 - - + -
105C PRO* 5.1 2.0 - - - -
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Residues in contact with GLN 13 (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 ALA 2.9 19.6 + - - +
10C GLU* 3.3 31.3 - - - +
12C VAL* 1.3 73.3 - - - +
14C GLU* 1.3 60.8 + - - +
16C LEU* 3.4 14.6 + - + +
17C SER* 2.9 28.9 + - - -
34C ARG* 6.2 1.3 - - - +
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Residues in contact with GLU 14 (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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13B ARG* 2.7 54.9 + - - +
14B LYS* 5.2 8.3 + - - +
17B ARG* 3.0 26.1 + - - +
36B MET* 4.6 16.2 - - + -
10C GLU* 2.9 19.4 + - + +
11C PRO 3.6 4.4 - - - +
13C GLN* 1.3 78.8 - - - +
15C GLU* 1.3 63.7 + - - +
17C SER* 3.2 5.6 + - - -
18C VAL* 2.9 37.0 + - + +
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Residues in contact with GLU 15 (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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14B LYS* 4.7 12.1 - - - +
11C PRO 2.9 14.6 + - - +
12C VAL 3.1 8.3 + - - +
14C GLU* 1.3 77.8 + - - +
16C LEU* 1.3 59.8 - - + +
18C VAL* 3.2 7.6 + - - +
19C LEU* 2.9 44.0 + - + +
64C LEU* 4.2 3.6 - - - +
68C TYR* 2.4 38.7 + - - -
105C PRO* 3.2 25.0 - - + +
107C VAL* 3.1 36.7 + - - +
108C HIS 3.9 4.0 + - - -
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Residues in contact with LEU 16 (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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12C VAL* 2.9 29.8 + - + +
13C GLN* 3.6 14.1 - - + +
15C GLU* 1.3 77.3 - - + +
17C SER* 1.3 57.8 + - - +
19C LEU* 3.4 4.9 + - + -
20C ALA* 2.9 30.6 + - - +
29C TRP* 3.7 31.2 - - + -
31C VAL* 5.7 1.3 - - + -
34C ARG* 3.7 30.3 - - - +
40C THR* 4.3 20.6 - - + +
42C PHE* 3.9 24.7 - - + -
64C LEU* 4.2 7.9 - - + -
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Residues in contact with SER 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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30B LYS* 3.9 5.4 + - - -
34B GLY 3.6 10.9 + - - -
35B THR 3.3 6.9 + - - -
36B MET* 3.2 46.4 + - - +
13C GLN 2.9 17.8 + - - -
14C GLU* 3.5 5.4 - - - -
16C LEU* 1.3 76.7 - - - +
18C VAL* 1.3 61.8 + - - +
20C ALA* 3.2 9.7 + - - +
21C ALA* 3.0 22.2 + - - +
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Residues in contact with VAL 18 (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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10B ALA* 4.1 15.0 - - + -
13B ARG* 5.2 6.7 - - + -
14B LYS* 4.7 14.6 - - - +
28B PRO* 6.3 0.4 - - + -
36B MET* 4.1 22.4 - - + -
38B LEU* 4.3 13.7 - - + -
14C GLU* 2.9 38.2 + - + +
15C GLU* 3.6 6.1 - - - +
17C SER* 1.3 76.5 - - - +
19C LEU* 1.3 58.8 + - + +
21C ALA* 2.9 3.9 + - - +
22C ILE* 2.8 49.0 + - + +
108C HIS* 5.2 0.7 - - + +
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Residues in contact with LEU 19 (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 GLU* 2.9 37.1 + - + +
16C LEU* 4.4 2.9 - - + -
18C VAL* 1.3 75.0 - - + +
20C ALA* 1.3 63.6 + - - +
21C ALA 3.1 1.2 + - - -
22C ILE* 4.4 7.2 - - + -
23C PHE* 3.0 45.5 + - + -
29C TRP* 3.4 33.4 - - + -
42C PHE* 4.1 5.2 - - + -
107C VAL* 3.6 26.0 - - + -
108C HIS* 3.8 41.5 - - + +
111C VAL* 5.1 1.3 - - + -
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Residues in contact with ALA 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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34B GLY 5.3 1.6 - - - +
35B THR* 4.0 25.5 - - + +
16C LEU 2.9 18.5 + - - +
17C SER* 3.2 8.7 + - - +
19C LEU* 1.3 74.6 - - - +
21C ALA* 1.3 56.8 + - - +
23C PHE 2.9 18.0 - - - +
28C GLU* 5.0 2.1 - - - +
29C TRP* 3.6 33.9 - - + +
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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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6B LEU* 4.0 17.5 - - + +
35B THR* 4.9 3.1 - - - -
36B MET* 3.0 37.7 - - + +
38B LEU* 4.6 9.6 - - + -
17C SER 3.0 10.6 + - - +
18C VAL* 2.9 9.7 + - - +
20C ALA* 1.3 75.4 - - - +
22C ILE* 1.3 66.7 + - - +
23C PHE 3.1 11.0 + - - +
24C CYS* 4.0 4.7 + - - +
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Residues in contact with ILE 22 (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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3B GLY* 5.6 3.3 - - - +
6B LEU* 3.9 38.7 - - + +
7B SER* 4.6 12.6 - - - +
10B ALA* 3.9 2.2 - - + -
38B LEU* 4.4 2.5 - - + -
18C VAL* 2.8 39.9 + - + +
19C LEU* 3.8 9.4 - - + +
21C ALA* 1.3 72.8 - - - +
23C PHE* 1.3 83.0 + - + +
24C CYS* 3.7 2.4 + - - -
25C ARG* 5.6 1.9 - - - -
108C HIS* 3.3 46.4 - - + +
112C LEU* 6.5 1.1 - - + -
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Residues in contact with PHE 23 (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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19C LEU* 3.0 40.2 + - + +
20C ALA 2.9 24.6 - - - +
21C ALA 3.1 2.0 - - - +
22C ILE* 1.3 97.7 - - + +
24C CYS* 1.3 57.7 + - - +
25C ARG* 4.2 26.7 - - - +
28C GLU* 2.7 32.1 - - + +
29C TRP* 4.2 17.7 - + + -
44C ILE* 3.4 41.1 - - + -
45C HIS 5.4 0.2 - - - -
46C THR* 4.8 5.8 - - - -
108C HIS* 6.0 0.9 - + - -
111C VAL* 3.9 26.0 - - + -
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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