Contacts of the helix formed by residues 13 - 31 (chain B) in PDB entry 1VZJ
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 GLU 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLN* 3.4 15.4 - - - +
10B TRP 3.2 7.3 + - - +
11B LYS 3.2 1.2 - - - -
12B ALA* 1.3 79.0 - - - +
14B PHE* 1.3 64.4 + - - +
15B HIS 3.5 0.6 + - - -
16B ARG* 3.8 18.4 + - - +
17B TRP* 3.5 20.2 + - - +
14C PHE* 3.5 36.8 - - + -
17C TRP* 3.9 24.6 - - + -
18C SER* 5.3 1.6 + - - -
9I LEU* 4.2 9.4 - - + -
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Residues in contact with PHE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 5.6 9.9 - - + -
10A TRP* 5.9 4.9 - + - -
13A GLU* 3.7 37.7 - - + -
10B TRP 4.0 3.6 + - - +
11B LYS* 3.2 16.9 + - - +
13B GLU* 1.3 77.4 - - - +
15B HIS* 1.3 70.6 + - - +
17B TRP* 3.3 29.0 + + - +
18B SER* 3.0 38.7 + - - -
8I PRO* 5.7 2.9 - - + -
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Residues in contact with HIS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LYS 4.6 0.8 + - - -
12B ALA 4.1 7.4 + - - +
13B GLU 3.5 1.2 - - - -
14B PHE* 1.3 84.0 - - - +
16B ARG* 1.3 67.8 + - + +
18B SER* 3.3 4.7 + - - -
19B SER* 3.0 30.3 + - - -
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA 5.1 1.2 + - - +
13B GLU* 3.8 18.3 + - - +
14B PHE 3.3 0.2 - - - -
15B HIS* 1.3 82.9 - - + +
17B TRP* 1.3 65.3 + - - +
19B SER* 2.9 11.1 + - - -
20B TYR* 2.9 63.2 + - + -
17C TRP* 6.3 2.9 - - + -
21C MSE 5.6 7.0 - - - -
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Residues in contact with TRP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 3.5 43.1 - - + -
16A ARG* 4.5 0.9 - - - -
17A TRP* 4.1 4.3 - + - -
13B GLU 3.5 11.4 + - - +
14B PHE* 3.3 34.7 + + + +
16B ARG* 1.3 81.1 - - - +
18B SER* 1.3 69.0 + - - +
20B TYR* 3.0 8.8 + - - +
21B MSE 2.7 67.4 + - + +
17C TRP* 3.7 29.8 - + + -
21C MSE 4.1 13.7 - - + -
5I PRO* 4.6 2.1 - - + +
6I PRO 2.9 23.2 + - - -
8I PRO* 3.4 36.0 - - + -
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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
----------------------------------------------------------
16A ARG* 4.2 12.1 + - - -
14B PHE* 3.0 41.3 + - - -
15B HIS* 3.7 5.2 - - - -
17B TRP* 1.3 86.2 - - - +
19B SER* 1.3 53.4 + - - +
21B MSE 3.2 6.6 + - - +
22B VAL* 2.8 35.5 + - - +
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 3.0 26.0 + - - -
16B ARG* 2.9 16.0 + - - -
18B SER* 1.3 75.7 - - - +
20B TYR* 1.3 62.8 + - - +
22B VAL* 2.9 11.6 - - - +
23B HIS* 2.9 49.4 + - - -
25C LYS* 5.8 0.5 + - - -
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Residues in contact with TYR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 2.9 54.2 + - + -
17B TRP* 3.6 5.2 - - - +
19B SER* 1.3 78.4 - - - +
21B MSE 1.3 68.0 + - - +
23B HIS* 4.0 7.7 - - - +
24B TRP* 2.9 27.4 + - - +
21C MSE 3.7 37.8 + - + +
22C VAL* 6.1 0.2 - - - -
24C TRP* 3.5 31.9 - + + -
25C LYS* 3.1 58.4 + - + +
5I PRO* 3.7 8.7 - - + +
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Residues in contact with MSE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 3.6 28.5 - - - +
17A TRP* 3.7 19.5 - - - -
20A TYR* 3.2 31.8 - - + -
17B TRP* 2.7 46.2 + - + +
18B SER* 3.2 14.4 - - - +
20B TYR* 1.3 79.5 - - - +
22B VAL* 1.3 62.0 + - - +
24B TRP* 4.1 2.9 - - + -
25B LYS* 3.1 22.0 + - - +
4I PRO* 3.7 9.6 - - + -
5I PRO* 3.0 34.3 - - + +
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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
----------------------------------------------------------
16A ARG* 3.8 12.3 - - - +
18B SER* 2.8 23.7 + - - +
19B SER* 2.9 27.8 - - - +
21B MSE 1.3 71.0 - - - +
23B HIS* 1.3 76.1 + - + +
25B LYS* 3.2 17.1 + - + +
26B ASN* 3.1 35.0 + - - +
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Residues in contact with HIS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 2.9 40.0 + - - +
20B TYR* 4.0 6.5 - - - +
22B VAL* 1.3 85.0 - - + +
24B TRP* 1.3 63.1 + - - +
26B ASN* 3.4 8.9 + - - +
27B GLN* 3.2 23.0 + - - +
25C LYS* 5.2 12.6 + - - -
28C PHE* 4.1 21.0 - - + -
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Residues in contact with TRP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.3 48.5 - + - -
23A HIS* 5.6 0.2 - - + -
24A TRP* 4.1 8.3 - + + -
20B TYR 2.9 18.4 + - - +
21B MSE 3.8 2.2 - - + +
23B HIS* 1.3 73.5 - - - +
25B LYS* 1.3 72.7 + - - +
27B GLN* 3.5 1.3 + - - +
28B PHE* 2.9 61.7 + + + +
24C TRP* 4.1 20.6 - + + -
28C PHE* 4.0 16.3 - + - -
1I LEU* 3.8 16.9 - - + +
2I LEU* 2.9 26.5 + - + -
3I THR 4.2 0.7 - - - -
4I PRO* 3.2 42.7 - - + -
5I PRO* 4.3 4.0 - - + -
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Residues in contact with LYS 25 (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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16A ARG* 5.5 1.3 - - - +
20A TYR* 3.6 30.3 - - + +
21B MSE 3.1 14.9 + - - +
22B VAL* 3.2 21.9 + - + +
24B TRP* 1.3 86.2 - - + +
26B ASN* 1.3 84.9 + - - +
28B PHE* 2.9 20.4 - - + +
29B ASP* 2.9 28.0 + - - +
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Residues in contact with ASN 26 (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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22B VAL* 3.1 17.0 + - - +
23B HIS* 3.7 11.4 - - - +
25B LYS* 1.3 103.4 + - - +
27B GLN* 1.3 64.1 + - - +
29B ASP* 2.8 22.8 + - - +
30B HIS* 3.2 11.3 + - - +
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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
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23B HIS 3.2 13.6 + - - +
24B TRP* 3.8 3.6 - - + +
26B ASN* 1.3 79.4 - - - +
28B PHE* 1.3 62.0 + - - +
30B HIS* 3.6 7.1 + - - +
31B TYR* 3.3 40.6 + - + +
28C PHE* 2.9 35.8 - - + +
31C TYR* 5.0 5.0 + - - +
32C SER* 3.4 32.8 - - - +
1I LEU* 4.0 19.1 - - + +
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Residues in contact with PHE 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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23A HIS* 3.6 38.6 - + + -
24A TRP* 4.7 3.8 - + - -
27A GLN* 2.9 40.6 - - + +
28A PHE* 5.4 0.9 - + - -
24B TRP* 2.9 42.2 + + + +
25B LYS* 2.9 13.9 - - + +
27B GLN* 1.3 77.8 - - - +
29B ASP* 1.3 77.6 + - - +
31B TYR 3.3 20.8 - - - +
1I LEU* 3.2 31.4 - - + +
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 2.9 41.3 + - - +
26B ASN* 2.8 15.2 + - - +
28B PHE* 1.3 83.7 - - - +
30B HIS* 1.3 69.6 + - - +
31B TYR 3.7 3.8 - - - -
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Residues in contact with HIS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASN 3.2 6.8 + - - +
27B GLN* 3.8 11.2 - - + +
29B ASP* 1.3 80.9 - - - +
31B TYR* 1.3 89.0 + + + +
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Residues in contact with TYR 31 (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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27A GLN* 4.1 14.6 - - - +
27B GLN* 3.3 28.5 + - + +
28B PHE* 3.3 16.1 - - - +
29B ASP 3.3 4.2 - - - -
30B HIS* 1.3 114.7 - + + +
31C TYR 5.3 7.8 + - - -
32C SER* 6.1 0.7 - - - -
1I LEU* 4.3 29.8 - - + +
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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