Contacts of the helix formed by residues 16 - 32 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY 3.6 2.2 - - - -
15B ALA* 1.3 79.2 - - - +
17B PRO* 1.3 70.9 - - - +
18B SER 3.3 3.1 - - - -
19B GLY 2.9 4.4 + - - +
20B MET* 2.8 30.6 + - - +
49B GLY 3.8 0.4 - - - -
50B GLY 3.5 15.7 - - - -
166B CYS 5.1 0.2 + - - -
500B FAD 3.3 21.1 + - - -
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Residues in contact with PRO 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY* 1.3 83.3 - - - +
18B SER* 1.3 56.7 + - - +
20B MET* 3.7 10.1 - - + +
21B ALA* 2.9 29.6 + - - +
49B GLY* 3.6 13.9 - - - +
52B TRP* 4.0 13.2 - - + -
112B ILE* 4.3 10.1 - - + -
115B ARG* 5.5 0.5 + - - -
327B PHE* 4.0 17.5 - - + -
330B PHE* 3.9 17.5 - - + -
500B FAD 3.5 39.9 - - - +
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 1.3 72.9 - - - +
19B GLY* 1.4 57.1 + - - +
21B ALA* 3.2 4.2 + - - +
22B GLN* 2.9 26.3 + - - +
166B CYS* 3.9 16.5 - - - -
318B ILE* 3.5 36.1 + - - +
330B PHE* 3.6 20.7 - - - -
334B ALA* 4.8 0.2 - - - +
500B FAD 2.8 36.4 + - - -
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Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.0 6.2 - - - +
14B GLY 3.3 25.1 + - - -
15B ALA* 4.7 1.3 - - - -
16B GLY 2.9 6.4 + - - +
18B SER* 1.4 75.0 - - - +
20B MET* 1.3 64.7 + - - +
22B GLN* 3.3 2.7 + - - +
23B LEU* 3.0 30.1 + - - +
166B CYS* 3.7 16.5 - - - +
500B FAD 4.3 0.2 + - - -
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Residues in contact with MET 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 3.8 16.0 - - + +
16B GLY 2.8 24.5 + - - +
17B PRO* 3.7 9.6 - - + +
19B GLY* 1.3 74.8 - - - +
21B ALA* 1.3 58.1 + - - +
23B LEU* 3.2 8.4 + - + +
24B ARG* 2.8 32.8 + - - +
48B TRP* 3.7 36.3 - - + -
49B GLY* 4.2 8.1 - - - +
112B ILE* 4.1 24.5 - - + +
113B LYS* 4.3 4.0 - - + -
115B ARG* 5.0 2.7 - - - +
116B VAL* 3.3 47.3 - - + +
125B ILE* 5.7 1.6 - - + -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO 2.9 19.5 + - - +
18B SER 3.2 6.5 + - - +
20B MET* 1.3 75.6 - - - +
22B GLN* 1.3 56.9 + - - +
24B ARG* 3.6 1.7 - - - +
25B ALA* 2.7 32.1 + - - +
115B ARG* 4.1 9.5 - - - +
330B PHE* 4.2 13.5 - - + +
331B ASP* 3.4 25.6 - - - +
334B ALA* 3.8 14.1 - - + +
335B TRP* 4.2 2.6 - - - -
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 3.7 28.3 - - + -
18B SER 2.9 13.1 + - - +
19B GLY* 3.3 10.9 + - - +
21B ALA* 1.3 73.6 - - - +
23B LEU* 1.3 67.5 + - - +
25B ALA* 4.1 3.0 - - - +
26B PHE* 3.3 43.1 + - + -
164B VAL* 3.7 27.1 - - + +
166B CYS* 4.7 2.9 - - - -
318B ILE* 3.8 3.3 - - + +
334B ALA* 3.2 41.0 + - - +
337B ALA* 3.7 9.0 - - - +
338B ARG 4.0 5.1 - - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 3.5 23.6 - - + -
15B ALA* 5.9 0.2 - - + -
19B GLY 3.0 19.8 + - - +
20B MET* 3.2 9.6 + - + +
22B GLN* 1.3 74.4 - - - +
24B ARG* 1.3 63.3 + - - +
26B PHE* 3.0 7.2 + - - +
27B GLN* 3.0 22.0 + - - +
39B LEU* 3.9 17.0 - - + +
41B CYS* 4.2 12.8 - - + -
121B VAL* 3.8 30.9 - - + +
124B TYR* 3.9 22.7 - - + -
125B ILE* 3.7 35.9 - - + -
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET 2.8 19.1 + - - +
21B ALA 3.8 2.2 - - - +
23B LEU* 1.3 75.3 - - - +
25B ALA* 1.3 65.7 + - - +
27B GLN* 3.6 19.8 + - - +
28B SER* 3.0 37.4 + - - -
88B ASP* 2.9 33.7 + - - +
115B ARG* 3.7 48.1 + - - +
116B VAL* 4.7 8.7 - - + -
118B LYS* 5.6 5.1 - - - +
119B ALA* 3.3 31.2 - - + +
121B VAL* 4.5 3.4 - - - -
335B TRP* 4.1 10.9 - - + -
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA 2.7 21.8 + - - +
22B GLN* 3.7 7.2 - - - +
23B LEU 3.2 0.2 - - - -
24B ARG* 1.3 76.3 - - - +
26B PHE* 1.3 60.2 + - - +
28B SER* 3.4 1.2 + - - -
29B ALA 3.2 7.8 + - - -
334B ALA 4.0 19.5 - - - +
335B TRP* 3.6 33.0 - - + -
338B ARG* 2.9 31.6 + - + -
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.5 7.9 - - + -
12B ILE* 4.9 0.7 - - + -
22B GLN* 3.3 45.0 + - + -
23B LEU 3.0 7.4 + - - +
25B ALA* 1.3 75.7 - - - +
27B GLN* 1.3 66.7 + - - +
29B ALA* 3.1 9.9 + - - -
30B GLN* 3.2 8.5 + - - +
36B ILE* 3.5 25.5 - - + +
37B PRO* 3.5 35.4 - - + -
39B LEU* 3.8 35.9 - - + -
338B ARG* 3.5 30.3 - - + +
341B ILE* 4.0 24.5 - - + -
342B MET* 4.2 11.2 - - + -
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Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU 3.0 7.7 + - - +
24B ARG* 3.6 18.6 + - - +
26B PHE* 1.3 76.3 - - - +
28B SER* 1.3 55.9 + - - +
30B GLN* 3.0 19.1 + - - +
31B GLU* 2.8 53.1 + - - +
36B ILE* 4.7 3.8 - - - +
39B LEU* 5.5 0.4 - - - +
118B LYS 5.5 0.4 + - - -
119B ALA* 3.5 43.1 + - - +
121B VAL* 3.7 21.8 - - + -
124B TYR* 5.6 6.5 - - + +
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG* 3.0 31.1 + - - -
25B ALA 3.5 8.7 - - - -
26B PHE 3.2 0.2 - - - -
27B GLN* 1.3 73.0 + - - +
29B ALA* 1.3 67.3 + - - +
30B GLN 3.0 2.1 + - - -
31B GLU* 3.2 15.1 + - - +
32B LYS* 3.3 28.1 + - - +
335B TRP* 3.7 23.0 - - - -
338B ARG* 4.3 3.4 - - - -
389B ASP* 6.1 0.4 - - - -
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 3.2 4.1 + - - +
26B PHE 3.1 10.7 + - - +
28B SER* 1.3 78.8 - - - +
30B GLN* 1.4 61.8 + - - +
32B LYS* 3.3 15.9 + - - +
33B GLY 3.5 0.5 + - - -
34B ALA* 3.1 22.1 + - + +
36B ILE* 4.2 10.8 - - + -
338B ARG* 3.9 28.4 - - - +
342B MET* 4.3 2.9 - - - -
344B ARG* 4.0 21.7 + - - +
389B ASP* 5.6 1.8 - - - -
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Residues in contact with GLN 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PHE 3.2 10.4 + - - +
27B GLN* 3.0 19.4 + - - +
29B ALA* 1.4 73.5 - - - +
31B GLU* 1.3 62.7 + - - +
32B LYS 3.0 1.8 - - - -
33B GLY* 2.9 19.9 + - - -
34B ALA 3.6 18.6 - - - +
36B ILE* 3.6 31.6 - - + +
124B TYR* 4.5 11.0 + - - -
301D LEU* 3.6 16.5 - - + +
361D ARG* 3.7 1.7 + - - -
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN* 2.8 34.1 + - - +
28B SER* 3.2 9.6 + - - +
30B GLN* 1.3 80.3 - - - +
32B LYS* 1.3 56.5 + - + +
297D ARG* 3.1 39.3 + - - -
361D ARG* 2.7 31.1 + - - +
365D LEU* 3.7 17.8 - - + +
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 3.3 19.5 + - - +
29B ALA* 3.3 10.5 + - - +
30B GLN 3.0 0.8 - - - -
31B GLU* 1.3 81.3 - - + +
33B GLY* 1.3 55.9 + - - +
34B ALA 3.5 1.9 + - - -
389B ASP* 3.9 34.3 + - - +
358D MET* 3.6 18.4 - - - +
361D ARG* 3.7 7.5 - - - +
362D GLU* 4.2 12.8 - - + +
365D LEU* 3.9 20.9 - - + -
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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
------------------------------------------------------------
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