Contacts of the helix formed by residues 16 - 32 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLY 3.6 2.6 - - - -
15A ALA* 1.3 79.6 - - - +
17A PRO* 1.3 78.8 - - - +
18A SER 3.2 2.9 - - - -
19A GLY 3.1 2.2 + - - +
20A MET* 2.8 25.6 + - - +
49A GLY 3.7 0.9 - - - -
50A GLY 3.6 14.1 - - - -
166A CYS 5.1 0.2 + - - -
500A FAD 3.3 20.1 + - - -
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Residues in contact with PRO 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY* 1.3 83.9 - - - +
18A SER* 1.3 56.7 + - - +
20A MET* 3.4 11.0 + - + +
21A ALA* 2.8 29.5 + - - +
49A GLY* 3.4 16.6 - - - +
52A TRP* 4.0 8.7 - - + -
112A ILE* 4.3 8.7 - - + -
115A ARG* 5.5 0.5 + - - -
327A PHE* 3.9 29.8 - - + -
330A PHE* 4.0 11.4 - - + -
500A FAD 3.4 35.7 - - - +
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Residues in contact with SER 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 1.3 73.6 - - - +
19A GLY* 1.3 62.1 + - - +
21A ALA* 3.1 7.2 + - - +
22A GLN* 3.0 26.5 + - - +
166A CYS* 3.9 15.8 - - - -
318A ILE* 3.5 36.5 + - - +
330A PHE* 3.6 18.7 - - - -
334A ALA* 4.8 0.3 - - - +
500A FAD 2.6 32.4 + - - -
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 4.0 6.5 - - - +
14A GLY 3.3 25.1 + - - -
15A ALA* 4.8 1.8 - - - -
16A GLY 3.1 5.6 + - - +
18A SER* 1.3 75.8 - - - +
20A MET* 1.3 64.1 + - - +
22A GLN* 3.2 2.8 + - - +
23A LEU* 3.0 31.4 + - - +
166A CYS* 3.7 16.5 - - - +
500A FAD 4.4 0.4 + - - -
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Residues in contact with MET 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 3.8 13.8 - - + +
16A GLY 2.8 27.8 + - - +
17A PRO* 3.6 10.1 - - + +
19A GLY* 1.3 72.3 - - - +
21A ALA* 1.3 61.8 + - - +
23A LEU* 3.2 10.5 + - + +
24A ARG* 2.8 32.7 + - - +
48A TRP* 3.7 35.9 - - + -
49A GLY* 4.2 7.6 - - - +
112A ILE* 4.2 21.5 - - + +
113A LYS* 4.3 3.8 - - + -
115A ARG* 4.8 3.6 - - - +
116A VAL* 3.2 48.2 - - + +
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO 2.8 18.3 + - - +
18A SER 3.1 7.4 + - - +
20A MET* 1.3 76.7 - - - +
22A GLN* 1.3 57.9 + - - +
24A ARG* 3.7 1.4 - - - +
25A ALA* 2.9 29.8 + - - +
115A ARG* 4.0 13.0 - - - +
330A PHE* 4.2 14.8 - - + +
331A ASP* 3.4 21.3 - - - +
334A ALA* 3.6 14.3 - - + +
335A TRP* 4.0 2.9 - - - -
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.9 28.0 - - + -
18A SER 3.0 13.2 + - - +
19A GLY* 3.7 10.3 - - - +
20A MET 3.1 0.2 - - - -
21A ALA* 1.3 75.1 - - - +
23A LEU* 1.3 66.3 + - - +
25A ALA* 3.4 1.9 + - - +
26A PHE* 3.3 41.3 + - + -
164A VAL* 3.6 22.9 - - + +
166A CYS* 4.8 3.8 - - - -
318A ILE* 3.9 2.9 - - + +
334A ALA* 3.2 31.1 + - + +
337A ALA* 3.5 22.2 - - - +
338A ARG* 4.0 6.9 - - - +
341A ILE* 5.6 0.2 - - - -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.6 24.0 - - + -
15A ALA* 5.9 0.2 - - + -
19A GLY 3.0 20.7 + - - +
20A MET* 3.6 9.2 - - + +
22A GLN* 1.3 77.1 - - - +
24A ARG* 1.3 55.4 + - - +
26A PHE* 3.1 5.4 + - - +
27A GLN* 3.0 28.6 + - - +
39A LEU* 4.0 17.6 - - + +
41A CYS* 4.2 11.7 - - + -
121A VAL* 3.8 30.8 - - + +
124A TYR* 3.8 24.0 - - + -
125A ILE* 3.8 35.2 - - + -
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A MET 2.8 18.4 + - - +
21A ALA 3.7 2.9 - - - +
23A LEU* 1.3 72.8 - - - +
25A ALA* 1.3 65.4 + - - +
27A GLN* 3.4 19.7 + - - +
28A SER* 3.0 34.7 + - - -
88A ASP* 2.8 36.0 + - - +
89A TYR* 6.1 0.2 - - - +
115A ARG* 3.4 51.7 + - - +
116A VAL* 4.9 7.9 - - + -
118A LYS* 5.3 8.3 - - - +
119A ALA* 3.2 31.3 - - + +
121A VAL* 4.4 3.6 - - - -
335A TRP* 4.0 9.7 - - + -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 2.9 18.3 + - - +
22A GLN* 3.5 7.4 - - - +
24A ARG* 1.3 78.7 - - - +
26A PHE* 1.3 62.7 + - - +
28A SER* 3.4 0.9 + - - -
29A ALA 3.3 8.3 + - - -
334A ALA 3.9 19.3 - - - +
335A TRP* 3.6 31.0 - - + -
338A ARG* 2.9 31.5 + - + -
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 4.4 11.2 - - + -
12A ILE* 5.1 1.6 - - + -
22A GLN* 3.3 45.7 + - + -
23A LEU* 3.1 8.0 + - - +
25A ALA* 1.3 78.8 - - - +
27A GLN* 1.3 62.4 + - - +
29A ALA* 3.2 2.1 + - - +
30A GLN* 3.1 16.6 + - - +
36A ILE* 3.5 25.0 - - + +
37A PRO* 3.5 35.0 - - + -
39A LEU* 3.8 33.7 - - + -
338A ARG* 3.6 30.1 - - + +
341A ILE* 4.1 22.7 - - + -
342A MET* 4.2 9.2 - - + -
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Residues in contact with GLN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU 3.0 16.3 + - - +
24A ARG* 3.6 19.1 + - - +
25A ALA 3.3 0.2 - - - -
26A PHE* 1.3 75.2 - - - +
28A SER* 1.3 56.9 + - - +
30A GLN* 3.1 16.2 + - - +
31A GLU* 2.8 52.2 + - - +
36A ILE* 4.8 2.7 - - - +
39A LEU* 5.5 0.4 - - - +
118A LYS 5.7 0.4 + - - -
119A ALA* 3.4 42.8 + - - +
121A VAL* 3.8 15.0 - - + -
124A TYR* 5.7 6.3 - - + +
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 3.0 24.5 + - - -
25A ALA 3.5 10.8 - - - -
27A GLN* 1.3 78.2 + - - +
29A ALA* 1.3 66.7 + - - +
30A GLN 3.2 0.5 + - - -
31A GLU* 3.3 7.3 + - - +
32A LYS* 3.2 37.0 + - - +
335A TRP* 3.7 23.8 + - - -
338A ARG* 4.3 3.4 - - - -
389A ASP* 6.0 0.9 - - - -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA 3.3 8.5 + - - +
26A PHE 3.2 10.1 + - - +
28A SER* 1.3 79.0 - - - +
30A GLN* 1.3 62.7 + - - +
32A LYS* 3.2 14.8 + - - +
33A GLY 3.4 0.5 + - - -
34A ALA* 3.1 23.4 + - + +
36A ILE* 4.1 10.3 - - + -
338A ARG* 4.0 25.1 - - - +
342A MET* 4.3 2.5 - - - -
344A ARG* 4.2 19.0 + - - +
389A ASP* 5.6 1.8 - - - -
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE 3.1 11.5 + - - +
27A GLN* 3.1 17.5 + - - +
28A SER 3.0 0.6 - - - -
29A ALA* 1.3 74.6 - - - +
31A GLU* 1.3 67.1 + - - +
32A LYS 3.0 1.6 - - - -
33A GLY* 2.9 15.4 + - - -
34A ALA 3.6 18.2 - - - +
36A ILE* 3.8 30.0 - - + +
124A TYR* 4.6 9.5 + - - -
301C LEU* 3.9 10.8 - - + +
361C ARG* 3.8 5.9 + - - -
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLN* 2.8 38.2 + - - +
28A SER* 3.3 8.0 + - - +
30A GLN* 1.3 76.0 + - - +
32A LYS* 1.3 56.4 + - + +
33A GLY 3.2 0.2 - - - -
297C ARG* 3.0 39.9 + - - -
361C ARG* 2.9 30.6 + - - +
365C LEU* 3.7 18.8 - - + +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A SER* 3.2 25.2 + - - +
29A ALA* 3.7 10.1 - - - +
30A GLN 3.0 1.4 - - - -
31A GLU* 1.3 76.9 - - + +
33A GLY* 1.3 57.7 + - - +
34A ALA* 3.5 1.7 + - - -
389A ASP* 3.9 35.2 + - - +
358C MET* 3.8 16.1 - - - +
361C ARG* 4.0 8.1 - - - +
362C GLU* 4.2 12.8 - - + +
365C LEU* 4.0 17.9 - - + -
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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