Contacts of the helix formed by residues 31 - 50 (chain B) in PDB entry 4U7E
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 ASP 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B HIS* 2.9 27.0 + - + +
30B ARG* 1.3 78.2 - - - +
32B PRO* 1.3 62.7 - - - +
33B VAL* 3.0 23.4 + - - +
34B VAL* 3.0 24.5 + - + +
35B ALA 3.0 21.0 + - - -
89B HIS* 2.7 28.0 + - - -
93B TYR* 5.1 8.3 - - + -
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Residues in contact with PRO 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B HIS 3.5 1.5 - - - +
28B ASP 3.7 17.0 - - - +
29B LYS 3.9 10.3 - - - +
30B ARG 4.1 0.9 - - - +
31B ASP* 1.3 85.1 - - - +
33B VAL* 1.3 61.5 + - + +
35B ALA* 3.6 12.4 - - + +
36B TYR* 2.9 28.1 + - - +
70B LEU* 4.4 11.4 - - + +
74B LEU* 3.6 26.5 - - + +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASP* 3.0 12.1 + - - +
32B PRO* 1.3 74.9 - - + +
34B VAL* 1.3 67.0 + - - +
36B TYR* 3.3 5.8 + - - +
37B TYR* 3.0 43.8 + - + -
74B LEU* 4.5 3.6 - - + -
77B ASN* 3.6 35.7 - - - +
79B ALA* 3.7 19.7 - - + -
80B ILE* 4.3 7.9 - - + -
89B HIS* 3.7 25.8 - - + +
90B LEU* 4.2 1.3 - - + -
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B HIS* 3.9 25.1 - - + +
31B ASP* 3.0 31.2 + - - +
33B VAL* 1.3 74.7 - - - +
35B ALA* 1.3 64.1 + - - +
37B TYR* 3.3 0.5 + - - +
38B CYS* 2.9 42.4 + - - -
89B HIS* 4.2 11.4 - - + -
90B LEU* 4.1 14.6 - - + -
93B TYR* 3.7 24.9 - - + -
124B LEU* 3.9 15.5 - - + -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 3.3 21.7 - - - +
27B HIS* 3.8 16.1 - - - +
28B ASP* 3.3 26.9 - - - +
31B ASP 3.0 5.1 + - - -
32B PRO* 3.6 11.9 - - + +
33B VAL 3.3 0.2 - - - -
34B VAL* 1.3 77.4 - - - +
36B TYR* 1.3 62.2 + - - +
39B ARG* 3.2 33.5 + - - +
70B LEU* 4.5 4.3 - - + -
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 3.8 22.0 + - - +
32B PRO 2.9 17.9 + - - +
33B VAL* 3.6 4.0 - - - +
34B VAL 3.2 0.2 - - - -
35B ALA* 1.3 78.0 - - - +
37B TYR* 1.3 85.1 + + - +
39B ARG* 3.1 6.4 + - - +
40B LEU* 2.9 35.3 + - + +
67B LEU* 3.6 41.8 - - + +
70B LEU* 3.6 24.6 - - + +
71B LYS* 3.7 32.1 - - + +
74B LEU* 3.8 14.8 - - + -
80B ILE* 3.8 21.1 - - + -
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Residues in contact with TYR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.0 30.7 + - + +
34B VAL 4.3 0.2 - - - +
36B TYR* 1.3 90.8 - + - +
38B CYS* 1.3 60.6 + - - +
40B LEU* 3.5 22.0 - - + +
41B TYR 2.9 24.1 + - - -
79B ALA 2.7 28.8 + - - -
80B ILE* 3.6 29.8 + - + -
83B GLU* 4.8 4.7 - - - -
86B GLY* 3.9 9.7 - - - -
90B LEU* 3.4 35.4 - - + -
127B VAL* 3.4 10.9 - - + +
130B VAL* 4.5 3.5 - - + +
131B PHE* 3.4 33.6 - + + -
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Residues in contact with CYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B HIS* 3.6 11.8 - - - +
21B LEU* 5.6 0.2 - - - -
23B THR* 3.9 16.2 - - - -
24B ALA* 3.6 21.1 - - + -
34B VAL* 2.9 30.8 + - - +
37B TYR* 1.3 78.4 - - - +
39B ARG* 1.3 62.2 + - - +
41B TYR* 3.4 5.0 + - - +
42B ALA* 3.0 22.5 + - - +
90B LEU* 5.5 0.4 - - - -
124B LEU* 3.8 29.8 - - - -
127B VAL* 3.9 19.3 - - + -
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU 5.5 2.2 + - - -
7B LEU* 5.2 0.8 - - - +
21B LEU* 4.5 6.3 - - + +
24B ALA* 3.6 17.9 + - + +
25B GLN* 3.7 16.6 + - - +
28B ASP* 2.7 42.3 + - - -
35B ALA* 3.2 26.9 + - - +
36B TYR 3.1 8.8 + - - +
38B CYS* 1.3 75.4 - - - +
40B LEU* 1.3 60.7 + - - +
42B ALA* 3.2 7.9 + - - +
43B MET* 2.9 29.8 + - - +
63B LEU* 3.9 18.3 - - + +
66B GLN* 2.7 43.9 - - - +
67B LEU* 3.6 15.2 - - + +
70B LEU* 4.2 16.0 - - - +
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 3.5 32.7 - - + -
331A LEU* 3.6 30.7 - - + -
332A LYS* 4.9 14.6 - - + -
36B TYR* 2.9 27.1 + - + +
37B TYR* 3.1 36.5 + - + +
39B ARG* 1.3 75.6 - - - +
41B TYR* 1.3 63.0 + - - +
43B MET* 3.3 3.1 + - - +
44B GLN* 3.0 19.8 + - - +
67B LEU* 3.7 9.1 - - + +
130B VAL* 4.1 16.6 - - + +
131B PHE* 6.0 0.2 - - + -
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Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 4.1 7.2 - - + +
20B HIS* 3.5 45.1 + + + -
37B TYR 2.9 14.7 + - - +
38B CYS 3.7 2.9 - - - +
40B LEU* 1.3 75.0 - - - +
42B ALA* 1.3 66.9 + - - +
44B GLN* 3.3 3.2 + - + +
45B THR* 2.8 55.3 + - - +
48B LYS* 6.3 0.7 - - - -
126B ASP* 3.3 40.4 - - + +
127B VAL* 3.7 18.8 - - + -
129B THR* 3.4 14.4 - - - -
130B VAL* 3.4 20.3 - - + +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 3.5 25.8 - - + +
20B HIS* 5.2 0.7 - - + -
21B LEU* 3.6 36.3 - - + +
38B CYS 3.0 14.9 + - - +
39B ARG 3.2 7.4 + - - +
41B TYR* 1.3 81.8 - - + +
43B MET* 1.3 58.2 + - - +
46B GLY* 2.8 27.2 + - - -
60B LEU* 4.7 0.7 - - - +
63B LEU* 4.1 6.3 - - + +
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Residues in contact with MET 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 4.0 12.1 - - + -
328A PHE* 3.8 11.0 - - + -
39B ARG 2.9 16.4 + - - +
40B LEU 3.5 5.6 - - - +
42B ALA* 1.3 77.7 - - - +
44B GLN* 1.3 63.1 + - - +
46B GLY* 3.8 0.3 - - - -
47B MET* 3.0 51.3 + - + +
60B LEU* 3.5 50.2 - - + +
63B LEU* 3.6 17.2 - - + +
64B MET* 3.6 38.6 - - + -
67B LEU* 3.7 11.0 - - + -
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Residues in contact with GLN 44 (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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328A PHE* 3.5 33.5 - - + -
332A LYS* 6.0 0.6 - - - +
40B LEU 3.0 12.0 + - - +
41B TYR* 3.8 5.6 - - + +
43B MET* 1.3 75.9 - - - +
45B THR* 1.3 62.7 + - - +
47B MET* 3.5 15.0 + - + +
48B LYS* 3.3 46.8 + - - +
129B THR 5.3 2.9 + - - -
130B VAL* 3.6 32.1 + - + +
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Residues in contact with THR 45 (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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16B SER* 4.7 3.1 - - - +
17B ILE* 3.5 27.6 - - + -
41B TYR* 2.8 47.3 + - - +
44B GLN* 1.3 74.7 - - - +
46B GLY* 1.3 66.0 + - - +
48B LYS* 3.1 20.2 + - + +
49B ILE* 3.1 32.7 + - + +
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Residues in contact with GLY 46 (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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14B PHE* 3.4 30.1 - - - -
17B ILE* 4.5 4.8 - - - +
42B ALA 2.8 18.2 + - - -
43B MET 3.8 0.7 - - - -
45B THR* 1.3 77.9 - - - +
47B MET* 1.3 60.0 + - - +
49B ILE* 3.1 3.2 + - - -
50B ASP 3.0 23.0 + - - +
60B LEU* 4.0 11.2 - - - -
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Residues in contact with MET 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ASP 4.8 11.4 + - - +
322A ASP* 5.0 1.1 - - - +
324A LEU* 3.8 10.3 - - + +
325A SER* 3.7 36.1 - - - -
328A PHE* 3.4 40.8 - - + -
43B MET* 3.0 39.1 + - + +
44B GLN* 3.7 11.4 - - + +
46B GLY* 1.3 76.0 - - - +
48B LYS* 1.3 62.0 + - - +
49B ILE 3.4 0.3 + - - -
50B ASP* 3.8 5.5 + - - -
51B SER* 4.1 18.6 + - - -
60B LEU* 3.9 13.2 - - + +
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Residues in contact with LYS 48 (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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320A ASP 6.1 1.1 - - - +
41B TYR* 6.3 1.0 - - - -
44B GLN* 3.3 36.8 + - + +
45B THR* 3.1 20.7 + - + +
47B MET* 1.3 78.3 - - + +
49B ILE* 1.3 64.9 + - + +
129B THR* 5.9 1.2 + - - -
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 3.5 31.2 - - + +
14B PHE* 4.0 19.5 - - + -
16B SER* 3.6 23.8 - - - +
17B ILE* 5.3 2.0 - - + -
45B THR* 3.3 25.6 - - + +
46B GLY* 3.1 7.2 + - - +
48B LYS* 1.3 82.7 - - + +
50B ASP* 1.3 67.6 + - + +
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 4.1 11.2 + - + +
14B PHE* 3.2 22.4 - - + -
46B GLY 3.0 8.7 + - - +
47B MET 4.4 0.2 - - - -
48B LYS 3.6 1.4 - - - -
49B ILE* 1.3 91.5 - - + +
51B SER* 1.3 58.9 + - - +
52B LYS* 3.0 6.4 + - - +
53B THR* 2.5 51.8 + - - -
56B CYS* 3.3 19.8 - - - +
60B LEU* 3.7 1.0 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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