Contacts of the helix formed by residues 16 - 32 (chain C) in PDB entry 2XLR
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 GLY 16 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLY 3.5 3.0 - - - -
15C ALA* 1.3 79.1 - - - +
17C PRO* 1.3 71.5 - - - +
18C SER 3.3 2.5 - - - -
19C GLY 3.1 2.6 + - - +
20C MET* 2.9 30.4 + - - +
49C GLY 3.8 0.2 - - - -
50C GLY 3.6 13.7 - - - -
166C CYS 5.1 0.4 + - - -
500C FAD 3.3 22.3 + - - -
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Residues in contact with PRO 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLY* 1.3 83.5 - - - +
18C SER* 1.3 56.6 + - - +
20C MET* 3.6 10.8 + - + +
21C ALA* 2.9 28.8 + - - +
49C GLY* 3.5 16.8 - - - +
52C TRP* 3.9 9.6 - - + -
112C ILE* 4.2 9.2 - - + -
115C ARG* 5.6 0.3 + - - -
327C PHE* 3.8 31.9 - - + -
330C PHE* 4.0 8.2 - - + +
500C FAD 3.4 37.5 - - - +
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Residues in contact with SER 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO* 1.3 76.7 - - - +
19C GLY* 1.3 57.9 + - - +
21C ALA* 3.2 2.8 + - - +
22C GLN* 2.9 27.0 + - - +
166C CYS* 3.8 15.7 - - - -
318C ILE* 3.5 37.1 + - - +
330C PHE* 3.6 21.3 - - - -
500C FAD 2.6 31.7 + - - -
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Residues in contact with GLY 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 4.0 6.0 - - - +
14C GLY 3.2 26.4 + - - -
15C ALA* 4.7 1.3 - - - -
16C GLY 3.1 6.2 + - - +
18C SER* 1.3 74.1 - - - +
20C MET* 1.3 63.3 + - - +
22C GLN* 3.2 3.3 + - - +
23C LEU* 3.0 31.7 + - - +
166C CYS* 3.6 15.9 - - - +
500C FAD 4.4 0.2 + - - -
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Residues in contact with MET 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA* 3.7 16.2 - - + +
16C GLY 2.9 24.9 + - - +
17C PRO* 3.6 10.8 - - + +
19C GLY* 1.3 74.1 - - - +
21C ALA* 1.3 57.4 + - - +
23C LEU* 3.4 9.0 + - + +
24C ARG* 2.9 32.7 + - - +
48C TRP* 3.7 35.0 - - + -
49C GLY* 4.3 9.9 - - - +
112C ILE* 4.2 23.1 - - + +
113C LYS* 4.6 2.9 - - + -
115C ARG* 5.0 2.2 - - - +
116C VAL* 3.2 47.7 - - + +
125C ILE* 5.7 1.3 - - + -
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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
----------------------------------------------------------
17C PRO 2.9 19.5 + - - +
18C SER 3.2 5.8 + - - +
20C MET* 1.3 76.5 - - - +
22C GLN* 1.3 58.3 + - - +
24C ARG* 3.1 1.4 + - - +
25C ALA* 2.8 32.4 + - - +
115C ARG* 4.2 8.7 - - - +
330C PHE* 4.2 12.8 - - + +
331C ASP* 3.3 26.0 - - - +
334C ALA* 3.8 13.5 - - + +
335C TRP* 4.1 1.4 - - - -
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 3.7 30.5 - - + -
18C SER 2.9 13.1 + - - +
19C GLY* 3.2 7.8 + - - +
21C ALA* 1.3 77.8 - - - +
23C LEU* 1.3 60.9 + - - +
25C ALA* 4.1 0.8 - - - +
26C PHE* 3.3 49.4 + - + -
164C VAL* 3.6 28.3 - - + +
166C CYS* 4.8 3.8 - - - -
318C ILE* 3.8 3.1 - - - +
334C ALA* 3.1 37.8 + - + +
337C ALA* 3.6 10.5 - - - +
338C ARG* 3.9 7.9 - - - +
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 3.7 22.9 - - + -
15C ALA* 5.9 0.4 - - + -
19C GLY 3.0 20.0 + - - +
20C MET* 3.8 9.0 - - + +
22C GLN* 1.3 75.3 - - - +
24C ARG* 1.3 58.5 + - - +
26C PHE* 3.2 7.0 + - - +
27C GLN* 3.0 28.1 + - - +
39C LEU* 4.0 15.8 - - + +
41C CYS* 4.2 13.0 - - + -
121C VAL* 3.8 29.2 - - + +
124C TYR* 3.8 24.0 - - + -
125C ILE* 3.8 34.1 - - + -
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Residues in contact with ARG 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C MET 2.9 15.2 + - - +
21C ALA 4.0 3.4 - - - +
23C LEU* 1.3 75.2 - - - +
25C ALA* 1.3 67.0 + - - +
27C GLN* 3.6 20.4 + - - +
28C SER* 3.1 33.5 + - - -
88C ASP* 2.8 32.7 + - - +
115C ARG* 3.1 55.5 + - - +
116C VAL* 4.8 9.2 - - + -
118C LYS* 5.8 2.2 - - - +
119C ALA* 3.1 38.8 - - + +
121C VAL* 4.5 2.5 - - + -
335C TRP* 4.0 12.3 - - + -
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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
----------------------------------------------------------
21C ALA 2.8 16.3 + - - +
22C GLN* 3.6 8.3 - - - +
24C ARG* 1.3 77.7 - - - +
26C PHE* 1.3 61.6 + - - +
28C SER* 3.4 1.6 + - - -
29C ALA 3.2 7.6 + - - -
334C ALA 4.0 18.4 - - - +
335C TRP* 3.4 33.6 - - + -
338C ARG* 2.7 32.0 + - + -
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 4.5 8.3 - - + -
12C ILE* 5.0 1.1 - - + -
22C GLN* 3.3 43.2 + - + -
23C LEU 3.2 7.5 + - - +
25C ALA* 1.3 76.5 - - - +
27C GLN* 1.3 66.0 + - - +
29C ALA* 3.2 5.7 + - - +
30C GLN* 3.1 17.3 + - - +
36C ILE* 3.6 20.7 - - + +
37C PRO* 3.6 32.1 - - + -
39C LEU* 3.7 37.0 - - + -
338C ARG* 3.5 30.5 - - + +
341C ILE* 4.1 23.6 - - + -
342C MET* 4.1 10.3 - - + -
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Residues in contact with GLN 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU 3.0 15.7 + - - +
24C ARG* 3.6 17.4 + - - +
26C PHE* 1.3 76.4 - - - +
28C SER* 1.3 59.9 + - - +
30C GLN* 3.1 15.9 + - - +
31C GLU* 2.8 45.9 + - - +
36C ILE* 4.7 3.3 - - - +
39C LEU* 5.5 0.6 - - - +
119C ALA* 3.3 43.7 + - - +
120C GLY 5.6 0.4 - - - +
121C VAL* 3.8 13.0 - - + -
124C TYR* 5.6 7.4 - - + +
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Residues in contact with SER 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ARG* 3.1 25.7 + - - -
25C ALA 3.5 6.1 - - - -
27C GLN* 1.3 78.5 - - - +
29C ALA* 1.3 66.2 + - - +
30C GLN 3.2 0.5 + - - -
31C GLU* 3.3 7.7 + - - +
32C LYS* 3.3 37.8 + - - +
335C TRP* 3.7 22.5 + - - -
338C ARG* 4.3 2.7 - - - -
389C ASP* 5.5 0.5 + - - -
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ALA 3.2 3.3 + - - +
26C PHE 3.2 10.0 + - - +
28C SER* 1.3 78.8 - - - +
30C GLN* 1.3 59.2 + - - +
32C LYS* 3.4 14.6 + - - +
33C GLY 3.5 0.5 + - - -
34C ALA* 3.0 27.1 + - + +
36C ILE* 4.3 10.3 - - + -
338C ARG* 3.8 32.7 - - - +
342C MET* 4.5 2.5 - - - -
344C ARG* 4.2 18.5 + - - +
389C ASP* 5.6 1.8 - - - -
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Residues in contact with GLN 30 (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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26C PHE 3.1 10.4 + - - +
27C GLN* 3.1 18.6 + - - +
28C SER 3.1 0.4 - - - -
29C ALA* 1.3 73.3 - - - +
31C GLU* 1.3 63.8 + - - +
32C LYS 3.0 1.8 - - - -
33C GLY* 2.8 20.4 + - - -
34C ALA 3.7 17.0 - - - +
36C ILE* 3.7 32.2 - - + +
124C TYR* 4.5 10.9 + - - -
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Residues in contact with GLU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLN* 2.8 33.3 + - - +
28C SER* 3.3 8.9 + - - +
30C GLN* 1.3 78.6 + - - +
32C LYS* 1.3 58.5 + - + +
33C GLY* 3.2 3.2 + - - -
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Residues in contact with LYS 32 (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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28C SER* 3.3 23.8 + - - +
29C ALA* 3.7 10.3 - - - +
30C GLN 3.0 1.4 - - - -
31C GLU* 1.3 79.9 - - + +
33C GLY* 1.3 58.4 + - - +
34C ALA 3.5 1.5 + - - -
389C ASP* 3.7 33.0 + - - +
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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
------------------------------------------------------------
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