Contacts of the helix formed by residues 15 - 28 (chain H) in PDB entry 1ZMC
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 15 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H GLY 3.4 4.6 - - - -
14H SER* 1.3 80.2 - - - +
16H PRO* 1.3 78.1 - - - +
17H GLY 3.2 2.9 - - - -
18H GLY 2.7 11.2 + - - +
19H TYR* 2.9 15.0 + - - -
42H GLY 4.5 0.2 - - - -
43H GLY* 3.5 9.6 - - - -
480H FAD 3.2 24.5 - - - -
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Residues in contact with PRO 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452G HIS* 5.6 0.7 - - + +
15H GLY* 1.3 80.4 - - - +
17H GLY* 1.3 60.9 + - - +
19H TYR* 4.0 13.0 - - + -
20H VAL* 3.2 28.2 - - - +
42H GLY 4.0 8.5 - - - +
45H CYS* 3.6 26.0 - - + -
328H ALA* 3.7 18.8 - - + +
332H GLU* 3.5 28.2 - - + +
480H FAD 3.2 33.4 - - - +
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Residues in contact with GLY 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H PRO* 1.3 76.1 - - - +
18H GLY* 1.3 57.7 + - - +
21H ALA* 3.0 30.8 + - - +
147H ALA* 4.9 0.7 - - - -
318H ILE* 3.3 17.7 - - - +
331H ALA* 3.4 30.6 - - - +
332H GLU* 4.3 0.2 - - - -
335H GLY* 4.2 1.6 - - - -
480H FAD 2.9 16.0 + - - -
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Residues in contact with GLY 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H VAL* 3.6 13.4 - - - +
13H GLY 3.2 23.6 - - - -
15H GLY 2.7 13.4 + - - +
17H GLY* 1.3 69.0 - - - +
19H TYR* 1.3 59.4 + - - -
20H VAL 3.1 1.6 - - - -
21H ALA* 3.1 4.3 + - - +
22H ALA* 2.9 29.3 + - - +
34H CYS* 4.9 0.4 - - - -
147H ALA* 3.8 9.6 - - - +
480H FAD 3.8 3.2 + - - -
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Residues in contact with TYR 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392G SER* 5.7 0.2 + - - -
452G HIS* 5.5 4.0 - - - -
472G ILE* 4.7 0.2 - - + -
473G ASN* 2.5 34.5 + - - -
13H GLY 3.8 0.2 + - - -
14H SER* 3.8 20.9 - - - +
15H GLY 2.9 25.3 + - - -
16H PRO* 4.0 11.9 - - + -
18H GLY* 1.3 71.6 - - - -
20H VAL* 1.3 78.9 + - + +
23H ILE* 3.1 54.0 + - + +
42H GLY* 4.8 4.3 - - - -
46H LEU* 6.2 0.2 - - + -
103H ILE* 3.6 38.2 - - + +
106H LEU* 4.9 2.0 - - + -
107H PHE* 3.4 28.4 - - + -
332H GLU* 4.2 9.2 + - - -
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Residues in contact with VAL 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472G ILE* 4.1 16.4 - - + +
473G ASN* 5.3 0.7 - - - +
16H PRO 3.2 22.6 + - - +
17H GLY 4.3 0.7 - - - +
18H GLY 3.1 1.0 - - - -
19H TYR* 1.3 107.3 - - + +
21H ALA* 1.3 66.3 + - - +
22H ALA 3.2 0.2 - - - -
23H ILE* 3.9 4.2 - - - +
24H LYS* 3.0 23.7 + - - +
332H GLU* 3.9 28.0 - - + +
336H ILE* 3.5 34.3 - - + -
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Residues in contact with ALA 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H VAL* 4.4 2.2 - - + -
17H GLY 3.0 21.4 + - - +
18H GLY* 3.1 5.5 + - - +
20H VAL* 1.3 76.4 - - - +
22H ALA* 1.3 59.0 + - - +
24H LYS* 3.8 1.4 - - - +
25H ALA* 2.8 31.7 + - - +
145H LEU* 3.4 32.3 - - + -
318H ILE* 4.2 0.4 - - + -
335H GLY* 3.9 24.6 - - - +
339H VAL* 3.7 5.5 - - + +
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Residues in contact with ALA 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H VAL* 4.1 6.7 - - + +
18H GLY 2.9 15.7 + - - +
19H TYR 3.6 5.6 - - - +
21H ALA* 1.3 76.6 - - - +
23H ILE* 1.3 57.5 + - - +
25H ALA* 3.1 3.6 + - - +
26H ALA* 2.8 29.3 + - - +
32H THR* 3.8 22.7 - - + +
34H CYS* 4.2 9.2 - - + -
107H PHE* 4.0 18.6 - - + -
112H VAL* 4.1 12.1 - - + -
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Residues in contact with ILE 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472G ILE* 3.8 31.0 - - + +
19H TYR* 3.1 47.1 + - + +
20H VAL* 3.9 3.8 - - - +
22H ALA* 1.3 78.7 - - - +
24H LYS* 1.3 63.4 + - - +
26H ALA* 3.4 3.3 + - - +
27H GLN* 3.0 47.0 + - - +
106H LEU* 4.2 16.4 - - + +
107H PHE* 4.0 16.4 - - + -
110H ASN* 3.8 18.1 - - - +
112H VAL* 4.3 7.2 - - + -
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Residues in contact with LYS 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464G LEU* 4.1 23.0 - - - +
468G PHE* 3.9 43.1 - - - -
472G ILE* 3.8 19.7 - - + +
20H VAL 3.0 17.8 + - - +
21H ALA 3.8 2.9 - - - +
23H ILE* 1.3 76.8 - - - +
25H ALA* 1.3 64.9 + - - +
27H GLN* 3.1 13.1 + - - +
28H LEU* 2.9 34.0 + - + +
336H ILE* 4.1 21.6 - - + +
339H VAL* 3.8 19.3 - - + -
340H GLU* 3.9 23.1 + - - -
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Residues in contact with ALA 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 4.4 7.0 - - + -
21H ALA 2.8 19.2 + - - +
22H ALA* 3.3 5.4 - - - +
24H LYS* 1.3 76.6 - - - +
26H ALA* 1.3 63.0 + - - +
28H LEU* 2.9 15.3 + - - +
30H PHE* 3.3 31.7 + - + -
32H THR* 3.6 20.6 - - + +
339H VAL* 4.0 19.9 - - + +
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Residues in contact with ALA 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H ALA 2.8 15.0 + - - +
23H ILE 3.6 7.0 - - - +
25H ALA* 1.3 71.2 - - - +
27H GLN* 1.3 58.7 + - - +
29H GLY* 2.9 22.2 + - - -
30H PHE 3.5 9.4 - - - +
32H THR* 3.2 11.8 + - - +
110H ASN* 3.3 29.4 - - + +
111H LYS* 5.0 1.6 - - + -
112H VAL* 3.7 16.8 - - + +
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Residues in contact with GLN 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464G LEU* 5.9 0.2 - - - +
468G PHE* 3.5 34.5 - - + -
470G LYS* 3.8 36.9 + - + +
471G SER 3.0 28.4 + - - +
472G ILE* 4.2 3.4 + - - +
474G PHE 5.1 2.2 + - - -
23H ILE* 3.0 33.0 + - - +
24H LYS* 3.1 19.4 + - - +
26H ALA* 1.3 74.9 - - - +
28H LEU* 1.3 59.4 + - - +
29H GLY 3.3 0.4 + - - -
109H GLN* 6.1 0.2 - - - +
110H ASN* 3.4 26.9 + - - +
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Residues in contact with LEU 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468G PHE* 4.2 22.9 - - + -
24H LYS* 2.9 27.5 + - + +
25H ALA* 2.9 11.4 + - - +
27H GLN* 1.3 77.7 - - - +
29H GLY* 1.3 58.7 + - - +
30H PHE* 3.6 12.0 - - + -
339H VAL* 3.7 37.2 - - + +
340H GLU* 3.8 18.4 - - + -
343H ALA* 4.4 16.1 - - + +
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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