Contacts of the helix formed by residues 16 - 26 (chain C) in PDB entry 1LU9
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 SER 16 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B TYR* 3.9 0.2 - - - -
45B TYR* 6.1 0.9 - - - -
8C GLN* 3.3 7.3 + - - +
10C ASP* 2.9 16.2 + - - -
12C ASP* 6.1 0.4 - - - -
14C THR 3.6 0.6 + - - -
15C PRO* 1.3 69.5 - - - +
17C VAL* 1.3 62.7 + - - +
18C PHE* 3.2 12.1 + - - +
19C ASP* 3.0 40.8 + - - -
20C VAL* 3.2 18.9 + - - +
67C GLY* 5.7 0.9 - - - -
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Residues in contact with VAL 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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7B PHE* 3.9 21.5 - - + -
9B PHE* 4.5 1.3 - - + -
34B TYR* 3.2 35.0 - - + +
44B ALA 5.0 0.7 - - - +
45B TYR* 3.3 52.3 - - + +
48B GLY* 3.7 16.4 - - - -
49B THR* 3.9 10.3 - - + -
15C PRO 3.3 1.0 + - - -
16C SER* 1.3 72.7 - - - +
18C PHE* 1.3 63.4 + - - +
20C VAL* 3.1 6.7 + - - +
21C VAL* 3.1 21.5 + - - +
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Residues in contact with PHE 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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47B ASP 5.0 0.9 - - - -
48B GLY* 3.8 20.4 - - - -
51B TYR* 4.1 23.3 - + + -
52B THR* 3.4 26.5 - - + +
16C SER* 3.2 8.5 + - - +
17C VAL* 1.3 80.1 - - - +
19C ASP* 1.3 73.3 + - - +
21C VAL 3.4 0.5 + - - -
22C VAL* 3.1 35.9 + - + +
256C LYS* 3.9 34.1 - - - -
257C LEU* 4.1 11.9 - - + -
260C HIS* 4.1 3.6 - + - -
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Residues in contact with ASP 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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6C LEU* 5.4 2.3 - - - +
8C GLN* 3.5 20.5 + - - +
10C ASP* 4.6 3.1 - - - +
16C SER* 3.0 24.9 + - - +
17C VAL 3.3 0.2 - - - -
18C PHE* 1.3 84.1 - - - +
20C VAL* 1.3 58.7 + - - +
22C VAL* 4.2 0.7 - - - +
23C GLY* 3.0 25.5 + - - -
31C ILE* 4.6 0.9 - - - +
64C PHE* 3.5 32.1 - - + -
66C GLY* 4.7 3.8 - - - -
67C GLY 4.7 2.4 + - - -
95C ASP* 4.5 6.2 - - - +
97C ASN* 5.0 8.2 + - - -
98C GLY 5.5 2.3 + - - -
260C HIS* 3.4 25.6 + - - -
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Residues in contact with VAL 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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7B PHE* 3.9 12.1 - - + -
32B THR* 3.6 32.3 - - + +
34B TYR* 4.3 6.3 - - - +
8C GLN* 3.3 23.6 - - - +
15C PRO* 5.1 2.0 - - + -
16C SER 3.2 13.0 + - - +
17C VAL 3.1 7.0 + - - +
19C ASP* 1.3 75.5 - - - +
21C VAL* 1.3 67.3 + - - +
23C GLY 3.1 1.4 + - - -
24C TYR* 3.0 46.4 + - + -
31C ILE* 3.3 17.0 - - + +
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Residues in contact with VAL 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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5B LEU* 3.9 14.5 - - + +
7B PHE* 3.5 27.8 - - + -
48B GLY 3.7 14.1 - - - +
49B THR* 4.9 1.6 - - - -
52B THR* 3.2 28.0 - - - +
53B ARG* 3.8 27.1 - - - +
61B THR* 4.6 3.8 - - - +
17C VAL* 3.1 14.8 + - + +
18C PHE 3.8 5.2 - - - +
20C VAL* 1.3 78.3 - - - +
22C VAL* 1.3 61.9 + - - +
24C TYR* 3.2 3.8 + - - +
25C ASP* 3.0 25.7 + - - +
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Residues in contact with VAL 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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52B THR* 3.9 10.1 - - + +
18C PHE* 3.1 31.6 + - + +
19C ASP 4.2 0.7 - - - +
21C VAL* 1.3 76.5 - - - +
23C GLY* 1.3 57.2 + - - +
25C ASP* 3.6 5.7 - - - -
26C GLY* 2.8 26.7 + - - -
257C LEU* 3.6 25.8 - - + +
260C HIS* 3.4 40.2 - - + +
261C ARG* 3.6 25.8 - - + +
264C ILE* 4.4 2.1 - - + +
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Residues in contact with GLY 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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6C LEU* 4.4 5.6 - - - -
19C ASP 3.0 17.9 + - - -
20C VAL 3.1 4.4 + - - -
22C VAL* 1.3 78.1 - - - +
24C TYR* 1.3 59.8 + - - +
26C GLY* 3.2 8.0 + - - -
27C GLY 3.3 0.3 + - - -
28C ALA* 3.1 22.2 + - - +
31C ILE* 3.7 14.8 - - - -
260C HIS* 5.4 0.2 + - - -
264C ILE* 3.7 19.8 - - - +
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Residues in contact with TYR 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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3B LYS* 5.2 11.3 - - + +
5B LEU* 3.6 28.9 - - + -
7B PHE* 6.0 0.2 - + - -
30B HIS* 3.5 52.3 + + + +
31B ILE 5.5 1.4 + - - -
32B THR* 4.4 6.8 + - - -
53B ARG* 5.1 1.3 - - - +
20C VAL* 3.0 43.0 + - + -
21C VAL 3.2 6.0 + - - +
23C GLY* 1.3 72.9 - - - +
25C ASP* 1.3 63.4 + - - +
27C GLY* 2.9 19.9 + - - -
28C ALA 3.5 18.0 + - - +
29C ASP 3.9 4.7 - - - -
30C HIS* 3.9 2.0 + - - +
31C ILE* 3.3 43.4 + - + +
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Residues in contact with ASP 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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2B SER* 4.6 9.0 + - - -
3B LYS* 4.7 1.2 + - - +
52B THR 4.4 0.7 - - - +
53B ARG* 2.8 56.0 + - - +
57B GLU* 5.0 2.9 - - - +
21C VAL* 3.0 19.3 + - - +
22C VAL* 3.6 4.2 - - - +
24C TYR* 1.3 77.0 - - - +
26C GLY* 1.3 59.5 + - - +
27C GLY 3.1 1.0 + - - -
261C ARG* 3.7 37.3 + - - +
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Residues in contact with GLY 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 VAL 2.8 16.1 + - - -
23C GLY 3.2 4.9 + - - -
24C TYR 3.1 0.8 - - - -
25C ASP* 1.3 76.6 - - - +
27C GLY* 1.3 58.8 + - - +
28C ALA 3.7 0.2 - - - -
261C ARG* 3.3 27.1 - - - +
264C ILE* 4.0 6.2 - - - +
265C ALA* 3.3 32.5 + - - +
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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