Contacts of the helix formed by residues 12 - 29 (chain B) in PDB entry 6E8Z
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 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLY* 3.8 0.6 - - - -
11B SER* 1.3 75.8 - - - +
13B ASN* 1.3 61.2 + - - -
14B TRP 3.4 1.8 - - - -
15B GLY 3.9 4.6 - - - +
16B SER* 2.7 34.5 + - - -
63B TYR* 3.6 12.5 - - - +
92B VAL 4.9 2.0 + - - -
401B NAD 3.4 35.5 + - - -
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Residues in contact with ASN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY* 1.3 72.0 - - - +
14B TRP* 1.3 58.8 + - - +
16B SER* 4.0 1.6 - - - -
17B ALA* 3.2 21.5 + - - +
63B TYR* 3.3 25.8 + - + +
64B LEU* 3.6 15.4 - - - +
153B ALA* 3.3 17.6 - - - +
154B SER* 4.5 7.1 + - - +
401B NAD 3.0 46.8 + - - +
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Residues in contact with TRP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASN* 1.3 74.4 - - - +
15B GLY* 1.3 57.0 + - - +
17B ALA* 3.3 3.2 + - + -
18B ILE* 2.7 59.8 + - + +
92B VAL* 3.6 16.8 - - + -
118B LEU* 3.6 21.5 + - + +
147B LEU* 4.0 19.1 + - + +
151B ASN* 3.5 27.4 - - - -
153B ALA* 3.7 24.7 - - - -
156B VAL* 4.0 26.0 - - + -
186B PHE* 4.1 13.2 - + - -
401B NAD 3.0 69.2 + + + +
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Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.4 4.2 - - - +
10B GLY 4.2 8.3 - - - -
11B SER* 4.6 3.6 - - - -
12B GLY 3.7 9.3 + - - +
13B ASN 3.5 0.4 - - - -
14B TRP* 1.3 78.3 - - - +
16B SER* 1.3 57.0 + - - +
18B ILE* 3.2 5.0 + - - +
19B ALA* 2.8 28.6 + - - +
38B MET* 4.8 1.6 - - - -
92B VAL* 3.6 31.5 + - - +
401B NAD 4.2 1.4 + - - -
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER* 3.3 4.3 + - - -
12B GLY 2.7 23.7 + - - -
13B ASN 4.0 0.4 - - - -
15B GLY* 1.3 75.6 - - - +
17B ALA* 1.3 63.1 + - - +
19B ALA* 3.0 18.0 + - - +
20B LYS* 3.2 9.7 + - - +
38B MET* 4.8 5.6 - - - +
60B ASN* 3.1 31.7 + - - +
63B TYR* 4.5 0.2 - - - +
64B LEU* 3.7 27.4 - - - +
69B LEU* 3.6 13.1 - - - +
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASN 3.2 16.6 + - - +
14B TRP* 3.3 6.9 + - + +
16B SER* 1.3 78.6 - - - +
18B ILE* 1.3 64.6 + - - +
20B LYS* 3.1 20.5 + - - +
21B ILE* 3.7 8.5 + - - +
64B LEU* 3.9 10.2 - - + +
153B ALA* 3.6 30.7 - - + +
156B VAL* 4.4 7.7 - - + +
157B ALA* 4.1 15.8 - - + +
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.7 8.1 - - + -
14B TRP* 2.7 49.9 + - + +
15B GLY* 3.6 5.2 - - - +
17B ALA* 1.3 72.3 - - - +
19B ALA* 1.3 58.9 + - - +
21B ILE* 3.2 13.1 + - + +
22B VAL* 2.9 42.8 + - + +
90B ILE* 4.6 11.4 - - + -
92B VAL* 5.9 0.2 - - + -
118B LEU* 3.6 30.1 - - + -
147B LEU* 5.0 1.1 - - + -
156B VAL* 5.3 0.2 - - + -
181B MET* 4.3 18.6 - - + -
186B PHE* 4.4 14.4 - - + -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.6 24.2 - - + -
15B GLY 2.8 14.4 + - - +
16B SER* 3.0 13.9 + - - +
18B ILE* 1.3 74.9 - - - +
20B LYS* 1.3 63.3 + - - +
22B VAL 4.4 0.4 - - - +
23B GLY* 2.9 23.4 + - - -
38B MET* 4.1 15.3 - - - -
69B LEU* 4.4 9.0 - - + -
70B PRO* 3.8 6.0 - - - +
73B VAL* 4.1 12.8 - - + +
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B SER 3.2 6.5 + - - +
17B ALA 3.1 8.9 + - - +
19B ALA* 1.3 76.3 - - - +
21B ILE* 1.3 65.5 + - + +
24B GLY* 3.5 4.9 + - - -
64B LEU* 4.2 12.8 - - + -
67B HIS* 3.0 25.7 + - + +
68B LYS 3.5 20.8 - - - +
69B LEU* 3.7 20.6 - - + +
70B PRO* 3.4 24.3 - - + +
156B VAL 6.1 0.7 - - - +
157B ALA* 3.0 35.9 + - + -
159B GLU* 5.5 5.1 + - - +
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA 3.7 7.2 + - - +
18B ILE* 3.2 12.8 + - + +
20B LYS* 1.3 79.2 - - + +
22B VAL* 1.3 66.9 + - + +
24B GLY* 3.1 3.1 + - - -
25B ASN* 2.9 37.8 + - - +
156B VAL* 3.6 31.6 - - + +
181B MET* 3.3 26.9 - - + +
183B THR* 3.4 17.0 - - + +
186B PHE* 3.8 31.6 - - + -
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 4.0 22.7 - - + -
8B ILE* 4.3 7.0 - - + -
18B ILE* 2.9 39.2 + - + +
19B ALA 4.3 1.1 - - - +
21B ILE* 1.3 78.9 - - + +
23B GLY* 1.3 57.3 + - - +
25B ASN* 3.3 0.9 + - - +
26B ALA* 2.8 33.6 + - - +
36B VAL* 4.3 12.8 - - + -
90B ILE* 4.2 8.7 - - + -
180B LEU* 3.8 31.3 - - + +
181B MET* 4.2 18.2 - - + -
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA 2.9 16.6 + - - -
22B VAL* 1.3 78.2 - - - +
24B GLY* 1.3 61.2 + - - +
26B ALA 3.3 0.2 + - - -
27B ALA* 3.0 20.3 + - - +
36B VAL* 4.4 5.1 - - - +
70B PRO* 4.0 8.7 - - - -
72B ASN* 3.0 18.9 + - - -
73B VAL* 3.8 22.3 - - - +
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS 3.5 11.0 + - - -
21B ILE 3.1 6.6 + - - -
23B GLY* 1.3 77.1 - - - +
25B ASN* 1.3 63.8 + - - +
27B ALA* 3.5 5.3 + - - +
28B GLN* 3.1 24.8 + - - +
70B PRO* 3.8 7.6 - - - +
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Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 2.9 26.8 + - - +
22B VAL 4.0 0.2 - - - +
24B GLY* 1.3 77.9 - - - +
26B ALA* 1.3 58.9 + - - +
28B GLN* 4.5 8.8 - - - +
29B LEU* 3.1 43.0 + - + +
32B PHE* 4.2 1.5 - - - -
179B GLU 3.6 13.6 + - - +
180B LEU* 3.0 35.4 + - - +
181B MET 3.8 0.2 - - - -
182B GLN 3.0 26.3 + - - +
183B THR* 4.1 4.1 - - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 5.2 1.8 - - + -
22B VAL 2.8 19.0 + - - +
23B GLY 3.9 1.1 - - - +
25B ASN* 1.3 75.7 - - - +
27B ALA* 1.3 54.7 + - - +
29B LEU 3.6 1.9 - - - +
32B PHE* 3.4 24.1 - - + +
33B ASP 3.8 9.6 - - - +
34B PRO* 3.8 6.8 - - + +
36B VAL* 3.5 26.9 - - + -
72B ASN* 4.7 0.2 - - - +
180B LEU* 4.4 8.7 - - + +
404B K 2.7 26.7 - - - -
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY 3.0 16.8 + - - +
24B GLY* 3.7 5.2 - - - +
26B ALA* 1.3 76.4 - - - +
28B GLN* 1.3 64.3 + - + +
34B PRO* 4.3 11.7 - - + +
72B ASN* 3.9 17.6 - - + +
404B K 3.0 12.5 - - - -
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Residues in contact with GLN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY 3.1 17.6 + - - +
25B ASN* 3.3 9.5 + - - +
27B ALA* 1.3 80.4 - - + +
29B LEU* 1.3 73.5 + - + +
30B ALA 3.8 1.2 + - - -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASN* 3.1 26.9 + - + +
26B ALA 3.6 2.3 - - - +
28B GLN* 1.3 94.0 - - + +
30B ALA* 1.3 60.0 + - - +
31B GLN* 3.2 20.2 - - - +
32B PHE* 3.3 24.7 + - + +
179B GLU* 3.5 35.2 - - + +
404B K 2.5 24.6 - - - -
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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