Contacts of the helix formed by residues 16 - 28 (chain C) in PDB entry 5LEZ
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 LEU 16 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C THR* 4.1 5.4 - - + -
9C VAL 3.6 19.5 - - - +
10C PHE* 3.7 25.8 - - + -
14C GLY 3.9 0.2 + - - -
15C HIS* 1.3 73.8 - - - +
17C PHE* 1.3 63.7 + - - +
18C GLN 3.4 1.8 - - - -
19C VAL* 3.1 36.5 + - + +
20C GLU* 3.2 15.5 + - - +
119C THR* 5.2 0.2 - - - +
81D LEU* 3.7 24.0 - - + -
84D ASP* 5.2 0.4 - - - +
135D ARG* 3.7 47.1 - - - +
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Residues in contact with PHE 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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9C VAL 4.2 6.2 + - - +
11C SER* 3.3 33.2 - - - +
12C PRO 5.4 1.3 - - - -
15C HIS* 3.6 30.9 + - + -
16C LEU* 1.3 73.2 - - - +
18C GLN* 1.3 59.2 + - + +
20C GLU* 3.3 21.1 + - - -
21C TYR* 2.8 67.8 + + + +
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Residues in contact with GLN 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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11B ILE* 3.7 21.5 - - - +
12B PHE* 2.9 62.1 + - - +
7C ILE* 3.5 25.8 - - + +
8C THR* 3.5 24.5 - - - +
9C VAL 5.6 0.6 + - - +
16C LEU 3.3 1.2 + - - -
17C PHE* 1.3 77.6 - - + +
19C VAL* 1.3 52.2 + - - +
21C TYR* 3.2 14.1 + - - +
22C ALA* 2.8 32.7 + - - +
125C ARG* 4.1 7.1 - - - +
126C PRO* 4.0 7.4 - - + +
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Residues in contact with VAL 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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8C THR* 4.0 7.4 - - + -
16C LEU* 3.1 30.6 + - + +
18C GLN* 1.3 72.1 - - - +
20C GLU* 1.3 66.7 + - + +
22C ALA* 3.1 9.7 + - - +
23C GLN* 3.0 34.0 + - - +
119C THR* 3.7 32.1 - - + -
126C PRO* 4.1 5.4 - - + -
149C PRO* 4.5 2.0 - - + -
150C SER* 3.8 35.4 - - - +
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Residues in contact with GLU 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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15C HIS* 3.0 45.4 + - - +
16C LEU 3.2 9.3 + - - +
17C PHE* 3.7 24.3 - - - +
19C VAL* 1.3 77.9 - - + +
21C TYR* 1.3 68.1 + - + +
23C GLN* 3.3 19.7 + - - +
24C GLU* 3.1 24.7 + - - +
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Residues in contact with TYR 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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12B PHE* 3.6 19.5 - - + -
13B SER 3.2 26.9 - - - +
14B PRO* 3.6 44.9 - - + +
16B GLY* 3.1 14.9 - - - -
17C PHE* 2.8 59.8 + + + +
18C GLN* 3.6 15.7 - - - +
19C VAL 3.2 0.2 - - - -
20C GLU* 1.3 81.6 - - + +
22C ALA* 1.3 62.9 + - - +
24C GLU* 3.1 8.0 + - + +
25C ALA 3.1 16.1 + - - -
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Residues in contact with ALA 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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12B PHE* 3.6 27.7 - - + -
18C GLN 2.8 13.3 + - - +
19C VAL 3.4 9.0 - - - +
21C TYR* 1.3 78.0 - - - +
23C GLN* 1.3 56.4 + - - +
25C ALA* 3.1 22.6 + - - +
26C VAL* 3.2 11.8 + - - +
126C PRO* 4.1 7.4 - - + -
127C PHE 3.8 19.1 - - - +
128C GLY* 4.0 2.2 - - - -
149C PRO* 3.8 10.8 - - + -
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Residues in contact with GLN 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 VAL* 3.0 30.3 + - - +
20C GLU* 3.4 24.0 - - - +
22C ALA* 1.3 72.7 - - - +
24C GLU* 1.3 65.6 + - - +
26C VAL* 3.2 10.4 + - + +
27C LYS* 3.1 31.9 + - + +
148C ASP* 3.1 27.1 + - + -
149C PRO* 4.0 15.7 - - + -
150C SER* 4.2 4.0 - - - -
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Residues in contact with GLU 24 (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 PRO 3.7 17.9 - - - +
15B GLU* 3.6 21.3 - - - +
20C GLU 3.1 15.5 + - - +
21C TYR* 3.1 10.5 + - + +
23C GLN* 1.3 72.5 - - - +
25C ALA* 1.3 67.0 + - - +
27C LYS* 3.1 43.2 + - - +
28C LYS* 3.4 18.9 + - - +
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Residues in contact with ALA 25 (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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12B PHE* 4.4 2.9 - - + -
15B GLU 4.9 0.7 - - - -
16B GLY* 3.8 23.0 - - - +
21C TYR 3.1 7.2 + - - +
22C ALA* 3.1 18.9 + - - +
24C GLU* 1.3 77.5 - - - +
26C VAL* 1.3 59.8 + - - +
28C LYS* 3.4 14.6 + - - +
29C GLY* 3.4 8.0 + - - -
75C GLY* 3.9 8.7 - - - -
76C LEU* 4.3 15.4 - - + +
128C GLY* 4.1 17.5 - - - +
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Residues in contact with VAL 26 (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 ALA 3.2 13.5 + - - +
23C GLN* 3.2 9.6 + - + +
25C ALA* 1.3 75.3 - - - +
27C LYS* 1.3 62.7 + - + +
29C GLY* 3.0 18.0 + - - -
74C ALA* 3.8 9.6 - - + +
75C GLY* 4.0 7.2 - - - -
129C ILE* 3.5 16.6 - - - +
130C SER* 3.4 43.5 - - - +
149C PRO* 3.9 11.2 - - + -
161C ILE* 4.9 1.8 - - + -
162C GLY* 3.4 25.0 - - - +
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Residues in contact with LYS 27 (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 GLN* 3.1 17.1 + - + +
24C GLU* 3.1 42.0 + - - +
25C ALA 3.3 0.4 - - - -
26C VAL* 1.3 81.3 - - + +
28C LYS* 1.3 58.6 + - + +
162C GLY* 4.3 9.2 - - - +
163C ARG* 3.0 29.4 - - - +
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Residues in contact with LYS 28 (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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15B GLU* 3.2 29.9 + - - -
16B GLY 4.6 5.1 + - - -
17B ARG* 3.9 19.8 - - - +
24C GLU* 3.4 10.2 + - - +
25C ALA* 3.4 9.9 + - - +
26C VAL 3.3 0.6 - - - -
27C LYS* 1.3 75.5 - - + +
29C GLY* 1.3 62.9 + - - +
30C SER 4.0 0.2 + - - -
163C ARG* 4.3 14.0 + - - +
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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